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Inner workings of browser based real-time MMO games

So, suppose there was a game which consisted of a website, and a client that you can launch from said website. I've looked a bit and a relatable example would be Habbo Hotel.
What I'm asking is, what are all the different parts that would make such a game work: for the website part, I'd imagine a server, a database, and some HTML, CSS and PhP coding would be required, but how would the client side operate?
More specifically, how would the client-to-server (and vice versa) real-time communications happen?
Suppose the client be coded in C, how would the integration of C into a (I suppose PhP-framed) browser window be executed?
Note that the client is never downloaded on the user's PC, so where would it reside?
I'm sorry if these are a lot of questions, if the answers were to be too tedious to compose, feel free to just leave some documentation or tutorials (which I've looked for but haven't really been able to find), I'll happily read them on my own. Thanks in advance.

On one side your question is too broad but on the other side I can give you some pointers of how to do this in a modern way:
don't have a client, just a page in a browser
use HTML5 canvas, you may also want to look into SPA (single page application)
connect via websocket, there are HTML5 javascript implementations and PHP or node.js for the server-side
best is, use node.js on the server, PHP would be way too cumbersome
via websocket, send and receive JSON objects
host node.js on its native platform (Linux)
you may want to look into phaser as an HTML5 client-side canvas rendering framework, but it lacks many functionality and is mainly oriented towards twitch-based action games, which don't work well with this architecture because of lag
this will lead you to one conclusion: javascript is at the center of this system. you'll encounter several roadblocks, such as:
security on websockets with SSL for login
avoid SSL for real-time data (above 1 Hz)
UI on the client inside the canvas is not easy to implement, you'll have to re-invent the wheel or find a UI library for that
expect lag, the network code will take some 20%-30% overhead in respect to native C/C# code using TCP/IP or UDP (Lidgren?) and protobuf (Lidgren+protobuf) is what high-frequency AAA titles use (MMORPG or FPS alike)
From the questions you asked I sense a great lack of understanding and knowledge about the field. I guess you'll have to study some 6-12+ months beforehand. This is what I recommend, because if you start right away you'll make a lot of errors and waste your time. If above are any names you don't know about, search them and study them well. And don't start to code, there is a very steep learning curve ahead of you!
EDIT: more about server-side
If you want to implement an action-based interactive game (like an FPS or 2D shooter) I have to tell you this.
You may want to look into Unity 3D, using directly TCP/IP connections and binary messages (no HTTP, no websocket, instead protobuf).
C# (client-side) and node.js (server-side) are a good combination. For horizontal scaling you may want to look into cloud computing, docker, provisioning and a lot of server security.
But this is hostile terrain, it leads you into DevOps territory, which is way off game development. More like an architect's job. Imagine that 3-tier system (client + server + database) has a bottleneck on the server.
You want to spawn more nodes to handle more clients. This is what EVERY lobby-based game does (LoL, Overwatch, WoT, WoW instances, and so on) and what you do for partitioned maps (e.G. the "maps" in LOTRO, RIFT, many more MMORPGS). Also, to mirror (which means multiple instances of the same map to accomodate an overpopulated crowd).
To have this kind of horizontal scaling your servers must go online/offline on their own without you clicking around on command and control (e.G. puppet and similar software).
While this is the ultimate approach, it also has the most steep learning curve, especially because of security (advert DDOS, flooding, slow-loris, fake clients, and the list goes on). A new node must be "provisioned" on the fly (e.G. cloud-config) before it attaches to the cluster and goes online, so there's a whole new world of pain and learning.
The center-piece of such an elastic cloud-based server system is SSO (single sign-on).

Driving .NET/Server Side applications through strictly Client UX.

I've been developing in the .NET stack for the past five years and with the latest release of MVC3 and .NET 4.0 I feel like the direction I thought things were headed in were further confirmed.
With the innovative steps the client community has in such a short period of time, it seems like the best in class apps have a UX controlled by a majority of client events. For example, facebook.com, stackoverflow.com, google, www.ponched.com :), etc. When I say client events I am not talking about a server side control wrapped in an UpdatePanel to mask the postback. I am talking about doing all events and screen transitions on the client and use full postbacks only when really necessary. That's not to say things like .NET aren't essential tools to help control security, initial page load, routing, middle tier, etc.
I understand when working on a simple application or under aggressive time constraints using the controls and functionality provided by default by .NET (or other web dev frameworks) isn't practical if the project calls for it but it seems like the developers that can set themselves apart are the ones you can get into the trenches of Javascript/jQuery and provide seamless applications that have limited involvement from the (web) server. As developers we may not think our users are getting more sophisticated because of the big name web applications they are using on the reg but I am inclined to think they are.
I am curious if anyone shares this view or if they have another take on this? Some post lunch thoughts I figured I'd fire out there and see what I got back.

I share this view. We've ironically moving away from thin client and back to thick client, although this time around everything on the client is distributed on-demand via the server so obviously the maintenance overhead is nothing like it used to be.
Rich client-side functionality not only gives you fluid, responsive, interactive apps, but has the significant advantage for large scale sites and applications of being able to palm off a large chunk of processing resources to client browsers rather than having to process everything at their end. Where tens or hundreds of millions of users are involved, this amounts to a very large saving.
I could say more on the matter but time is short. I'm sure there will be other views (assuming the question isn't closed for being subjective).

The point about the developers who set themselves apart is definitely on target. Developers who understand the underlying technologies and can produce customized solutions for their clients are indeed set apart from developers who can drag and drop framework tools and wire up something that works well enough.
Focusing on web development in this discussion, it's vitally important that developers understand the key technologies in play. I can't count how many times I've encountered "web developers" (primarily in the Microsoft stack, since that's where I primarily work) who patently refuse to learn JavaScript/HTML/CSS simply because they feel that the tooling available to them in Visual Studio does the job just fine.
In many cases it does, but not in all cases. And being able to address the cases where it doesn't is what puts a developer above the rest. Something as simple as exposing a small RESTful JSON API and using AJAX calls to fetch just the necessary data instead of POSTing an entire page and re-processing the entire response means a lot to the overall user experience. Both get the job done, but one is considerably more impressive to the users than the other.
Frameworks are great when what you want to do is fully encapsulated in the feature set of the framework. But when you need to grow beyond the framework, it ends up being limiting. That's where a deeper understanding of the underlying technologies would allow a developer to grow outside of the framework tooling and produce a complete solution to the client.

You are right in saying that modern web development involves technologies like jQuery (or similar libraries) and JavaScript in general.
Full page reloads are old fashion and Ajax approach is the way to go, just don't think that the web server is less used or involved than before, it still responds to the ajax calls simply it does it asynchronously :)
MVC does not support any post back actually, because there are no web forms and there is not the same model of page life cycle.

Need help determining how to approach building my project

I'd like to create something similar to a family tree online app (like geni.com). I'm unsure what languages I should use to build it with. My IT strong points aren't in programming and this project is going to require me to sit down and learn some languages. My problem right now is that I don't know what languages I should use.
So with the idea of a family tree online app in mind here are some of the specifications.
- I do not want to use flash.
- The app needs to be zoomable and scrollable (sort of like google maps)
- The app needs to be able to add content without reloading the page. Perhaps there's a little "+" sign and when I click it, I can add a tag/title/description/picture
- The app needs to be able to save your work for that user to retrieve later on.
- The layout that a user is able to create in is sort of widget based where the user can add a new bubble and then in that bubble they are able to add text or content.
I started programming this with HTML5 canvas and Javascript, but I'm stuck on creating a connection to the database that isn't directly from Javascript (because that seems very insecure to me). But I'm not just stumped on how to interact securely with the database (I don't even have a database picked out), but also I'm concerned that I won't be able to build out the app with just javascript and may need something else like ajax or something but I'm unfamiliar with what each language does nowadays.

If you are starting from scratch, then the best language to use is the one you are most comfortable with. Alternately, if you don't plan to be developing the whole thing yourself and you already have some other interested parties on board then the best language to use is the one that the majority of you are comfortable with. If it's just you and you do not yet have any favorites, then look around and play with a few - it's the only way to find out if you will actually like / be effective with them.
That being said, a few of the more likely candidates these days are:
JavaScript: Long gone are the days when this language was simply a way to put the D in DHTML. These days JavaScript is a viable client and server-side language. (Others here have already recommended Node.js -- I'd also recommend NPM (node package manager) to handle your dependencies). With a little bit of planning you can reuse most of your application code on both the client and the server side. On the downside, most of the server side technology is very new (only a few years old at most) and so you may find yourself implementing tools for use in your application rather than your application itself. Finding servers that support it will also be harder, again on account of it's age.
Perl: At the opposite end of the spectrum of age, we find Perl - the first commonly deployed language used to make web applications it still powers a great variety of useful websites out there (include new ones such as Pinboard.) The tools that are popular on CPAN have been vetted under fire. The good news is that it is not going anywhere anytime soon. The bad news is, you might have to search a little harder to find a module that supports [that newest, baddest thing that just came out yesterday].
PHP: The BASIC (or Perl, depending on who you ask) of the modern web, PHP was designed from the ground up to do one thing - make building dynamic web pages easier. Its popularity means that there is quite a lot of server support (PHP + Apache + MySQL is the Model T Ford of web servers -- everyone can afford one) and an enormous amount of pre-built code available for perusal. However, like BASIC, PHP's strength is also its greatest weakness. Almost anyone can write something that works in PHP ... how well it works depends on who wrote it. The caveat emptor that applies to all code snippets found on the web applies in spades to snippets of code written in PHP.
Python: The language that made programing fun again (at least for those who can see past the significant whitespace and lack of blocks / anonymous functions and overlook < 3.x's issues with non-ASCII out of the box.) It's a general-purpose, flexible and multi-paradigm language with quite a substantial standard library (but without .NET or Java's incredible bloat). In addition, quite a large amount of work has been done in it, so there is a good chance that what you need has been already developed by somebody else. Plus, it can make you fly.
Ruby (with or without Rails): The language that made the web fun, coupled, if you so desire, with the framework that made MVC cool. There is lots of documentation out there, and a great community, with many prebuilt tools (called gems) from which to pick and choose - free and cheap servers are not as common as their PHP counterparts, but they are likely to be of higher quality (when chosen at random).
All that being said, they are all great languages for web development. What matters is not what we think you should use ... but what you are most likely to be effective with. All of the languages listed above are mainstream (or will be in the next two years), easy-to-learn and easy-to-write languages. You cannot go wrong, no matter what you choose to start off with.
Alternately, if you want something a little more difficult, or less mainstream ... I am working with .NET applications at work, and with Lisp (SBCL)-based services in my spare time. I have heard great things about Lua and Java too ... there are at least two C++ web frameworks out there ... and I'm sure that there is somebody is having fun building a web service in COBOL with a FORTRAN backend. ;-)

As someone has already pointed out, you will need to work with a server side language as well. (Ruby, Python, PHP) You are exactly right there you should not be attempting a database connection via javascript in the browser.
You'll need to build out a server side application to handle the basic operations of your application.
I'd strongly recommend reading up on the MVC design pattern, and possibly looking into Ruby on Rails as your backend framework, it plays very nicely with ajax like features, and has a somewhat shorter learning curve, I believe, than some other frameworks / languages.

You will need server side scripts in a language like PHP or Ruby on Rails to interact with a database.

If you're already familiar with HTML5 and JavaScript, may I recommend using Node.JS? It's about the closest you'll get to what you already know with browser development. It can also hook in with database systems which are closer to the HTML5-suggested IndexedDB.
with that in mind...
If you're inexperienced with programming and programming languages, then the app you describe will involve a pretty big learning curve. While Flash and Flex have really nice interfaces to build apps with click-and-drag, the tools for HTML5 are much less mature.
That's not saying it's not possible with HTML5. Just that there's still some time to wait before people create tools to bring the app building process closer to what Adobe provides.

Language to choose for a board game (flash or HTML5/JS)

I am developing a web based multi-player board game and wondering what the best language for the UI would be? Its a board game similar to Go but a lot simpler.
I have two options flash or the much touted HTML5 with JS. I have to learn both though I have basic knowledge of JS.
The problem with flash is I have to pay for the server component but the UI development could be easier and have a richer look and feel to it. With HTML5 + JS there is no cost involved but the UI development I feel will be clunky and not smooth. This I am not sure. Any experienced devs out there care to give some advice? Are there any particular issues to worry about, look into?
EDIT: Thanks for the comments. I will go with HTML5/JS.
As far as the server side goes, I have not yet decided what to use but want to look into node.js. May be I need to post it to programmers.stackoverflow.com about how it handles load and concurrent users.
Thanks,
Pav

Go with HTML and JS, you said your game was similar to GO, well check out http://govsgo.com/.
The site is written in JavaScript, well there's not much on the front end, the backend is based on Ruby on rails, check out Railscasts #237 (http://railscasts.com/episodes/243-beanstalkd-and-stalker) for some background info on the Ruby part.
You can even do really heavy stuff these days in JavaScript, like multiplayer asteroids (http://bonsaiden.github.com/NodeGame-Shooter/), so a "simple" game like you want to build, shouldn't be problem at all.

HTML5/JS will be less compatible with your audience. A lot of people still have non-compliant browsers.
That being said, HTML5/JS would be more fun I think. :)
http://html5readiness.com/ Provided by Robert Pitt

Is your game meant to be used on the iPhone? If yes, Flash is a no-go, as it is not available on the iPhone.

My vote: HTML5/JS.
Why? Consider:
Flash is fading away. On the other hand, you will enjoy a growing audience for your game (including iPhone, iPad and Android).
Flash is more expensive.
I am confident that you can create any UI in HTML5 that you can in Flash. In fact, and presumed limitations of HTML5 may actually force you to refine your UI in a positive way.
Have you seen Grooveshark since they recreated their entire application in HTML5 instead of Flash? Check it out as a proof of concept.
HTML5/JS is easy.
Flash requires a third party plugin, HTML5 only requires an up to date browser- which requirement is better for the user? Personally, I'd rather update my browser than install a third party plugin.

Since your making a multi-user game flash is the way to go. Multi-user stuff is possible with html5/js but as Chuck says its not available in all the browsers. For the multi-user side of things you can use Red5 (which is free) or SmartFox which is not free if you have more than 100 concurrent users. I built a big project with SmartFox awhile back and I found it really easy to work with. Depending on the simplicity of your game you could roll your own socket server code with a language of your choice.

Flash is pretty hard to learn unless you know Java or classic OO (I could add a lot to that comment). I would go with JS/HTML/CSS. As Chuck said, it would be more fun.
The server is only an issue if you plan to use Flash Interactive Server which is pricey. There are open source alternatives. But you say that as if JS has this built in - it doesn't. If you want real time updates, you'll need a CometD server and those are not easy to implement. I'd go with a short poll regardless of whether it's Flash or JS.

Web development with ESN Planet, how does it work?

I'm starting a new job soon, in web-app development. While I'm experienced with programming, my background is primarily in game development and desktop/server applications. I have very little experience from modern web app development. Anyway...
Our primary development tool is going to be something called ESN Planet, which I've not heard about before. Their website is not very specific about its features, and it seems unlikely for one to get a trial invitation ("We have been getting lots of applications, so please try to be as detailed as possible when applying for an invite below.").
Is anyone using this tool, and can explain what kinds of skills are involved in development of apps using this tool? Should I learn Python, JavaScript, CSS, or something else? All of the above? What is the workflow like for a developer? Will I need modern HTML skills?
I'd like to prepare for this job, but not sure what to expect and prepare for. My contact with the company is not a developer, so I figured I would ask here.

I saw a talk by the boss of the company that developed this stuff, at the Europython conference this year. It was ostensibly about the custom IDE that they created to develop in it, but also touched on the Planet system itself. It seems like a pretty run-of-the-mill MVC framework, as far as I can tell.
As far as what to learn, you will definitely need Python. Normally in web development you also need HTML, CSS and Javascript as well - but some frameworks abstract a lot of that away from you, to a greater or lesser extent. Impossible without knowing more about the framework to tell whether this is one that does. And it also depends on the way the company you're working for is set up - some have separate front-end teams that deal with that side of things, leaving the Python developers to just manage the server-side stuff.

For what it's worth, ESN Planet has been used to build Battlelog (http://battlelog.battlefield.com), the web platform for stats tracking and web launching of Battlefield 3.