PDF has the advantage that it looks fantastic when printed out, and the 
disadvantage that it generally doesn't look very good on-screen. Being a 
paged medium, with (usually) portrate pages while the screen has a 
landscape aspect, it's really not very screen-friendly.

HTML has the opposite advantages: it looks terribly when printed out 
(I've yet to find any browser anywhere that can print HTML properly), 
but it's much easier to work with on-screen. It can use screen-optimised 
fonts, you can adjust the font size to look good on your screen, the 
text layout automatically matches the window size, and so on.

Of course, PDF has the advantage of being a single, compressed file with 
no possibility of broken hyperlinks / missing images / missing fonts / 
etc. But for a help file, I'd suggest that HTML is more appropriate. 
(Who the hell is going to print out 2,000 pages on actual paper?)

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