[auxym]

I used Zotero, mostly for it's automatic database filling feature (eg from a journal website). I sort-of classified papers in in a directory-like structure by topic. When it came time to find stuff, the search worked pretty well, considering most papers had the abstract filled out in zotero and therefore was indexed for searching.

Good support for shared libraries if you work with other people.

Combined with a plugin called lyz, it made for a very streamlined integration in my thesis workflow (in lyx).

Bonus: free and open source.