Computing being my job, and having some experience with web sites' building, I can't help saying this:
— Are you aware that relying on Javascript is bad for accessibility? Not that you can't use it, but the same features should be also available without Javascript.
— Same for the frames: they are bad for accessibility. Besides, they are deprecated in xhtml, which is the current state-of-the-art HTML (until HTML5 is ready).
— Finally, CHM is all but a standard format, although I can understand how it can be convenient to have one single file instead of a bunch of HTML, JS, CSS… files.
Well… to (kind of) answer your question, I don't know of any such tool, but (I'm not sure) I think I've seen a firefox extension once to save a whole page as a single file.
I hope this helps.
Yves.
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