http://www.zotero.org/

http://www.colwiz.com/

For OS X and Windows:

http://endnote.com/

http://www.mekentosj.com/papers/

http://pdfstacks.com/

For OS X:

http://bibdesk.sourceforge.net/

http://www.sonnysoftware.com/bookends/bookends.html

http://www.thirdstreetsoftware.com/site/SenteForMac.html

http://www.ironicsoftware.com/yep/

For Windows:

http://www.biblioscape.com/

http://www.citavi.com/

http://www.qiqqa.com/