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I've been using Zotero, though I'm still undecided how much I like it (but I do know know people who love it): http://www.zotero.org/

I dabbled with Zotero for research purposes awhile back, might have to give the latest version a spin to see if I can bend it to my needs.

I have tons of ebooks, word docs, ppt, PDFs, etc. though, and manually organizing them would probably(definitely) take too much time.

How are you using Zotero?