Mendeley is not bad at all. I save papers to a Dropbox folder, organized directories by general topic / relevance to project. Mendeley (on one computer) watches that folder, and imports the papers and fills out the bibliographic info, mostly automatically.

Mendeley lets you tag and organize things in virtual folders, as well as store notes and annotations. The bibliographic info for subsets of papers (eg. with a particular tag) can be exported to bibtex files when writing.

Mendeley is available on all platforms, and syncs across multiple computers. The only catch is that the links to PDFs are only maintained on the 'master' that watches the folder. (If you try to watch folders on multiple instances of the same synced database, all hell breaks loose.)

Pubchase (www.pubchase.com) can also sync with your Mendeley library, and does a surprisingly good job of recommending papers of interest.