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javascript encodeURIComponent and escape?

I use JS to sent encodeURIComponent string to a PHP file write and has been working fine for years; until recently I met with a strange effect that the text need to be further encoded with escape in order to get it to work! The sympton start to show only when I use an open source wysiwyg editor !
What could be the offending characters in URI that need escape to fix it? I used to think URI only reserve ? & = for its syntax to work.

The situation you describe could possibly be explained--although there's no way of knowing without you telling us what the string is, and how it's being used--by a URL which involves two levels of nested URL-like values.
Consider a URL taking a query parameter which is another URL:
http://me.com?url=http://you.com?qp=1
That URL is subject to misinterpretation, so we would normally URL-encode the you.com URL, giving us:
http://me.com?url=http%3A%2F%2Fyou.com%3Fqp%3D1
Whoever is working with this URL can now extract the query parameter named url with the value http%3A%2F%2Fyou.com%3Fqp%3D1, decode it (often a framework or library will decode it for you), and then use it to jump to or call that URL.
Consider, however, the case where the you.com URL itself has a query parameter, not ?qp=1 as given in the first example, but rather something that itself needs to be URL-encoded. To keep things simple, we'll just use "cat?pictures". We'd need to encode that, making the query parameter
In other words, the URL in question is going to be
?qp=cat%3Fpictures
If we just use that as is, then our entire URL becomes
http://me.com?url=http%3A%2F%2Fyou.com%3Fqp=cat%3Fpictures
Unfortunately, if we now decode that in a naive way, we get
http://me.com?url=http://you.com?qp=cat?pictures
In other words, the nested URL has been decoded as well, meaning that it will think the URL has two query paramters, namely url and qp. To successfully deal with this problem, we need to encode the second query parameter a second time, yielding
http://me.com?url=http%3A%2F%2Fyou.com%3Fqp%3Dcat%253Fpictures
Please note, however, that if you use your language or environment's built-in tools and libraries for handling query parameters, most of this will happen automatically and prevent you from having to worry about it.
The symptom start to show only when I use an open source wysiwyg editor
An editor merely places characters in a file. It's very hard to imagine that an editor is causing the problem you refer to, unless perhaps one editor is configured to use smart quotes, for example, which would pretty much break everything that involved quotes.

How to remove executable JavaScript from a QueryString variable?

I have a page URL something like this: https://site.com/page.aspx?QSVariableName=Value
Our security team has raised a vulnerability stating that if the Value portion is injected with executable JS, that is something like:
https://site.com/page.aspx?QSVariableName=Value%27%2balert%281234567890%29%2b%27 (Equivalent to passing Value'+alert(1234567890)+')
Then 1234567890 is alerted from the OnClick event of a hyperlink I have on the page that uses Value.
Like I said, this is not something I am doing intentionally, but is identified as a vulnerability in the code. So the question is, how do I make sure QSVariableName uses just the Value and ignore unnecessary code (lets keep to JS only for now)?
The complexity that comes to my mind is QSVariableName could contain ANY JS code, not just alert(). And it could be present anywhere, not just at the end. Is there any way to identify JS executable code embedded in a string?
It is OK if Value is a bad 'string' as long as it doesn't contain anything executable.

What if, instead of putting QSVariableName directly into the onclick attribute, you used a switch/case pattern to choose a function based on QSVariableName? You could also map appropriate query strings to appropriate functions using an associative array. Either way, you'd only ever be treating QSVariableName as a string and only be using safe and pre-approved JS in your onclick event. The downside being, anyone who tries to inject JS into the query string will get an error, but they're trying to hack your site...their user experience should suffer accordingly.
Without seeing more of your code, I'm not sure I can come up with a better answer...

Should I worry that using GET in a form element doesn't automatically URL-encode angle brackets?

So I decided to use GET in my form element, point it to my cshtml page, and found (as expected) that it automatically URL encodes any passed form values.
I then, however, decided to test if it encodes angle brackets and surprisingly found that it did not when the WebMatrix validator threw a server error warning me about a potentially dangerous value being passed.
I said to myself, "Okay, then I guess I'll use Request.Unvalidated["searchText"] instead of Request.QueryString["searchText"]. Then, as any smart developer who uses Request.Unvalidated does, I tried to make sure that I was being extra careful, but I honestly don't know much about inserting JavaScript into URLs so I am not sure if I should worry about this or not. I have noticed that it encodes apostrophes, quotations, parenthesis, and many other JavaScript special characters (actually, I'm not even sure if an angle bracket even has special meaning in JavaScript OR URLs, but it probably does in one, if not both. I know it helps denote a List in C#, but in any event you can write script tags with it if you could find a way to get it on the HTML page, so I guess that's why WebMatrix's validator screams at me when it sees them).
Should I find another way to submit this form, whereas I can intercept and encode the user data myself, or is it okay to use Request.Unvalidated in this instance without any sense of worry?
Please note, as you have probably already noticed, my question comes from a WebMatrix C#.net environment.
Bonus question (if you feel like saving me some time and you already know the answer off the top of your head): If I use Request.Unvalidated will I have to URL-decode the value, or does it do that automatically like Request.QueryString does?
---------------------------UPDATE----------------------------
Since I know I want neither a YSOD nor a custom error page to appear simply because a user included angle brackets in their "searchText", I know I have to use Request.Unvalidated either way, and I know I can encode whatever I want once the value reaches the cshtml page.
So I guess the question really becomes: Should I worry about possible XSS attacks (or any other threat for that matter) inside the URL based on angle brackets alone?
Also, in case this is relevant:
Actually, the value I am using (i.e. "searchText") goes straight to a cshtml page where the value is ran through a (rather complex) SQL query that queries many tables in a database (using both JOINS and UNIONS, as well as Aliases and function-based calculations) to determine the number of matches found against "searchText" in each applicable field. Then I remember the page locations of all of these matches, determine a search results order based on relevance (determined by type and number of matches found) and finally use C# to write the search results (as links, of course) to a page.
And I guess it is important to note that the database values could easily contain angle brackets. I know it's safe so far (thanks to HTML encoding), but I suppose it may not be necessary to actually "search" against them. I am confused as to how to proceed to maximum security and functional expecations, but if I choose one way or the other, I may not know I chose the wrong decision until it is much too late...

URL and special caracters
The url http://test.com/?param="><script>alert('xss')</script> is "benign" until it is read and ..
print in a template : Hello #param. (Potential reflected/persisted XSS)
or use in Javascript : divContent.innerHTML = '<a href="' + window.location.href + ... (Potential DOM XSS)
Otherwise, the browser doesn't evaluate the query string as html/script.
Request.Unvalidated/Request.QueryString
You should use Request.Unvalidated["searchText"] if you are expecting to receive special caracters.
For example : <b>User content</b><p>Some text...</p>
If your application is working as expected with QueryString["searchText"], you should keep it since it validate for potential XSS.
Ref: http://msdn.microsoft.com/en-us/library/system.web.httprequest.unvalidated.aspx

Encoding uri component, do not automatically decode

I have users with slahes in their usernames. I want to give them easy urls such as /user/username even if their username is problematic. ie /user/xXx/superboy.
I'm using client side routing and I don't think there's any wildcard support. One obvious way to fix this would be to encode their username. href="/user/xXx%2Fsuperboy". But the browser automatically decodes the url when going to the link and then my router ends up not matching anyway. Is there some way to keep the browser from automatically decoding the url or any other way to solve my problem (perhaps a different decoding scheme?). Thanks.
I'm using angularjs with angular ui-router for routing.

Part 1.
Automatic decoding of URIs can be encounted in many situations, such as it being interpreted once then the interpretation passed on (to be re-interpreted).
Part 2.
In a path in a URI, / has a special meaning, so you can't use it as the name of a file or directory. This means if you're mapping something that isn't a real path to a path, you may end up with unexpected characters causing problems. To solve this the characters need to be encoded.
As you want to map usernames to a URI, you have to consider this might happen, so you have to encode in a way that allows for this. From your question, it looks like this happens once, so you'll need to double encode any part of the URI that isn't a "real URI path".
Also maybe you can explain how reliable this is and whether it's advisable
If you always have it used in the same way, it should be reliable. As for advisable, it would be much better to use the query part, rather than the path for this. href="/user?xXx/superboy" is a valid URI and you can get the query string easily (everything after first ?, or an inbuilt method). The only character you'd have to watch for is #, which has special meaning again.

How to show a friendly error message using Open-flash-charts2?

If my JSON data-file comes from a database result set and that result set is empty, how do I tell OFC2 to display an error message, instead of crashing because of a malformed JSON string?

Add tags for javascript and actionscript-3 to this question and you should get a load more views and useful responses than you currently are, with more precise details than I am giving. Post the actual JSON string that is causing you the problem and that you would like to be guarded against. That way people can suggest a regexp to catch it, treating it as a string rather than as JSON data at some point before JSON.decode() happens.
In more detail:
You can catch it in two places. One route is to switch over to using the javascript interface to OFC2 and use client side javascript to detect the bad string. This allows you to modify the JSON string client side. See http://teethgrinder.co.uk/open-flash-chart-2/tutorial-5.php for that approach. One downside is that the clients must have javascript enabled for this to work.
Alternatively, since OFC2 is LGPL, you or an actionscript developer can dive into the OFC2 source code and do the same thing there. I am not an actionscript developer so you are better off ensuring you get a reply from one.
The main thing is to add those two tags to this question. 22 Views is way too low for a question with a bounty of 500. Hope this helps.

Several solution avenues are possible, depending on your level of access to the server and your knowledge of JavaScript and/or any server-side platforms.
With access to database
Depending on the kind of data you are displaying, it might be possible to add dummy records for those queries that would otherwise have returned an empty set. If you have access to the query definition, you may check for the empty set in the DB-query. For example, if you're on MS SQL Server you could check the condition with some T-SQL statements.
With access to server
If you have access to the server side script generating the dataset, add a condition that returns some default value that OFC2 will handle correctly.
With access to another server or serverlocation
If you don't have access to the specific script, you may consider creating a new script at another location that queries the original script and replaces empty results with the default value.
Client-side only
You can add the JavaScript open_flash_chart_data function (see tutorial) to replace empty datasets. OFC2 can use that function as data source.
Hope this helps.