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Does setPointerCapture works only for pointerDown event?

MDN says:
The setPointerCapture() method of the Element interface is used to designate a specific element as the capture target of future pointer events. Subsequent events for the pointer will be targeted at the capture element until capture is released.
And it works as expected if I call setPointerCapture in pointerDown callback: example - here you can drag yellow square as fast as you want and it will follow the cursor until pointerUp event happens.
But if try to capture target in pointerMove callback it won't work as I expected: example - yellow square follows the cursor until cursor hovers the square. If you move your mouse too fast square will stopped.
How this behavior can be explained? Did i misunderstand the documentation?

Not exactly.
The specs ask that
The pointer MUST be in its active buttons state for this method to be effective, otherwise it fails silently.
To be in its active buttons state means:
The condition when a pointer has a non-zero value for the buttons property. For mouse, this is when the device has at least one button depressed. For touch, this is when there is physical contact with the digitizer. For pen, this is when either the pen has physical contact with the digitizer, or at least one button is depressed while hovering.
So if your pointer device is in this state when you first move it over your element, or from any other event for that matter, it should work, until you release your pointer device.
However note that for your code to work in Firefox you need to preventDefault() the pointerdown event. But from Chrome, with a mouse device, you can start by dragging outside of the element, then move over it and the capture will work as intended.
The problem with your code is that it doesn't check if the capture did work, raising the captured flag unconditionally. Instead of this flag, check for element.hasPointerCapture(e.pointerId).

Drag, drop and mousewheel?

Short version: Can mouse wheel events be fired while in the middle of a drag+drop operation?
Long version:
I'm currently in the design phase for this particular feature, so I don't have any code yet. I'm asking this so I know if it's a waste of time to pursue this path, so I can design something else instead.
Basically, I have a list of items on one side, and a basket on the other. As it stands right now, each item has an input box and a button so you can type the quantity and add it to the basket (and same thing in reverse). I want to add drag and drop functionality so you can just drag items one way or the other. This works fine if you only want one of the item, but I'd like to add a way to adjust the quantity while dragging. The mouse wheel came to mind, since you're already using the mouse to drag in the first place.
So before I dive into the code, I need to know if it's actually possible to receive mouse wheel events during a drag, and if so where should I add the listener?

If you want to check if the primary mouse button is being pressed during a wheel event, you can use the following:
addEventListener('wheel', function (event) {
if (event.buttons & 1) {
alert("You scrolled while the primary mouse button was down!");
}
}
Unfortunately, if you're using the Drag and Drop API with the draggable='true' attribute, wheel and scroll events are not fired during a drag, so you will be unable to fire and handle a scroll event.

Enable mouseup / mousedown but prevent click behavior

I have a data visualization here (the second one):
http://mikeheavers.com/main/work
If you click on the circles representing skill fields, it reveals inner green circles with the particular skills. If you hold down on the green circles representing the skills, they animate, grow, and then shrink back on mouse release. However, if you simply click on the circles, they grow, but do not return to their previous size (the mousedown is not registered I guess) - which results in a circle that will constantly get bigger each time it is clicked.
Is there a way to prevent click behaviour, either through d3 or through Javascript / jQuery? I only want mouseup and mousedown.

I'm observing different behavior than what you described.
If you single click a circle, it doesn't matter how long the click is (whether it's held or not), it returns back to its original size.
If you click a circle repeatedly and quickly, this is when it starts to grow and does not return to its original size.
If you hold down a circle and then move your mouse outside of it, it both stays pink and doesn't return to its original size.
I think attaching a simple .on('mouseout', handler) to return spheres to their original size will solve the last issue, which is pretty glaring, and any missed mouseup events due to moving outside. You can also attach a mouseup to the whole document (d3.select('body').on('mouseup', handler)), which will catch any such event; then you would just need to record the last sphere that was clicked.
Additionally, to fix your original problem, you can make sure that mouseup events are triggered by adding e.preventDefault() in the mousedown events. This will prevent fast clicks from turning into double-clicks or other events by the browser.
Other posts that discuss these issues:
mouseup event isn't always triggered
mouseUp event on drag

Javascript IE mouse events restricted to original recipient?

I have an info overlay that works great in Chrome and FF. It is a div containing a table (for border image layout) and then a central content div. I trigger mousedown on the appropriate border table cells.
Once this happens, a different div is brought to the front with z-index, and that passes along the mousemove and mouseup events to handle dragging the info bubble around. Once the mouseup is fired, the info bubble puts the "event" div back to where it was.
I also follow the same process for dragging the lower right corner of the bubble to resize it. Again, works in Chrome and FF, but fails in IE.
IE seems to be restricting the event triggers to the info div. If the mouse manages to move outside the div (from dragging faster then the events fire/update), the info overlay no longer receives mousemove events. However, if I move the mouse back over the overlay (without releasing the button) it continues to receive mouse events.
Edit: In creating some example code (the current functionality is split across several JS modules), it worked in IE. As soon as I find the difference between my example code and the actual code, I will update again.
Edit/Answer: (SO wont let a new user answer their own question in this time span...)
Still not sure what the actual problem was. (If you ask me, a div with a z-index of 100 should be receiving mouse events just fine?)
My solution was to fix my mouse event handling such that I could attach my mousemove and mouseup to the parent div (as should have been done in the first place) for all dragging/resizing behaviors I wanted to set up.
The problem was due to a newbie approach to the events and having stopPropagation() in too many locations preventing me from taking such an approach. (I wanted text, etc in my info box to be selectable).
I adjusted the code so that my text containers only had to stop propagation on mousedown instead of all the mouse events.

mouseover fired with mouse still and element moving

I am in a situation where I need jQuery's mouseover event to be fired when an element (in this case an image) moves under the mouse, so unlike the common situation is an element that is moving, not the mouse.
Do you know of any library/gist/technology that could help me in this sense?
I've tried with flash but with no luck, is this something than can actually be done?

You can track mouse position by binding a handler to mousemove on the body, and calculate after every move of the image whether the pointer is over it.

I ran across a similar issue. In my case I did a "good enough" workaround by keeping track of the time the mouse last moved and then in the mouseover handler seeing if the mouse had moved recently -- within 30ms of the current time. That way I can bail out in cases where the mouse didn't actually move, but I don't have to test the hitboxes myself -- something very hard to do right and fast, and fortunately something I can leave to the browser by doing this.