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If you need a good-looking page for printing, you can use a print-only stylesheet to accompany the standard one on your HTML pages.
It's also nice to use id's for linking to specific parts of your documentation, which I don't think pdf's can do at this stage. Once your docs are loaded, they're cached so switching around to different id's with <a href="docs.html#thisid"> type url's goes real fast, documentation isn't completely reloaded.