Since the question is relatively fitting of the topic, and people keep mentioning mostly the same apps (so a lot of people have experience with them), I'll just ask it here.
Knowing that I already have Papers, what is the best replacement for Endnote? Could it be worth it to just stick with Endnote?
It all depends on what your writing platform is. For Word 2008, you can just use papers (and word's new built-in bibliography tool). For word 2004, you'll need endnote. For Mellel, Bookends, and for LaTeX, it's hard to do better than BibDesk. I think pages requires the latest Endnote X2.
EDIT: I'm really liking Mellel / Bookends / Papers as my workflow right now although I have used Word / Endnote and LaTeX (textmate) / BibDesk in the past.
Addendum: Zotero (a firefox plugin) is very effective and free for research and bibliography formatting. It is compatible with word and neo-office (but not neo-office 3 yet)
Addendum 2: Pages requires at least Endnote X2 2.0.1
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