You can organise your books/articles/chapters into folders to make it easier to find them, but you can also give them keywords so you can search on all the books you've tagged as <oulipo> or <teaching> or <genre>. You can even use Zotero to store notes on each book--although I can't quite bring myself to get into this--I prefer having my notes as text files which I can back up and double back up.
But my favourite feature is the way that you import things into Zotero. Rather than keying in author/title/publisher etc. etc., whenever your browser is open on a page containing a book and its reference details (say your browsing the BL catalogue, or Google Books, or an online journal), an icon of a book appears in the browser address bar:
and Zotero will import all the details into your database. If you've downloaded PDFs--say from JSTOR--you can also point Zotero at them, and it'll pull all the relevant referencing data into your library automatically.
Interfacing with Word or OpenOffice is as simple as it should be--dropping in references or creating a bibliography only takes a couple of clicks, as does switching between stylesheets.
Anyway, it should be obvious now that I've become a bit evangelical about the whole thing, so I'll leave off proselytising. But I would be interested to hear if anyone's got a different experience of EndNote. There's a similar application for the Mac too that I've heard good things about. Anyone?