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When a program stops responding, and turns gray and the box that says "this program is no longer responding" comes up, How do I know when to close the window, and when do I wait for it to respond?

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There isn't one answer fits all... this really comes down to your individual experience and the program involved.

Typically, a program will have this when it fails to respond to typical Windows GUI commands/events such as maximize/move e.t.c.

Typical reasons for this is that the program is single threaded and is currently busy processing a command (for example, saving).

Usually a program will come back to life upon it completing the task, but, there is just no way to know in advance - as much as it could be completing a very complex task, it can equally be likely that it is also in an infinite loop and will never recover!

Personally, I would say that if it is freezing in reaction to something I have done, I would wait (up to) at least a minute (e.g. click saving), but, if it is just random, and it isn't some intensive tasks I would say either give it a minute or conclude it is frozen.

Sorry I can not be more precise, but, there just isn't a single answer that fits everything.

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I don't think you could have been more precise... Thanks anyway. – wizlog Dec 11 '11 at 18:49
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@William: To really know whether it's looping or not, it's possible to attach a debugger like WinDBG and pause every now and then to look into it's stack. Or well, you can even do that with Process Explorer which is also able to show threads. When it's I/O related you can look into Process Monitor whether it is actually progressing to different files rather than looping the same (set of) file(s) again... – Tom Wijsman Dec 11 '11 at 20:28
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@TomWijsman +1 ... people are always saying it to me, so, my turn to say it back!...Why not blog about that? Sounds like it could be quite interesting! – William Hilsum Dec 11 '11 at 21:53
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@WilliamHilsum: If I only had the time to blog about all those things, I'm doing my best to find the time to be around SU these days. Perhaps the next semester will have a lot of free time, we'll see.. – Tom Wijsman Dec 11 '11 at 21:55
@TomWijsman hehe, know the feeling! – William Hilsum Dec 12 '11 at 0:35

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