Citation Managers

Which one do you use and why is it so great

• Zotero
  • free, open source
  • integrated with firefox: one click adding to your library
  • store pdf and fulltext snapshots with your citation
  • organize citations in collections
  • store data locally and online for easy access at multiple workplaces
  • (of course) easy import/export of bibtex
  • share citation collections in groups: distribute knowledge among your colleagues
• Mendeley Desktop
  • free, but not open source
  • available for mac, windows and various linux distributions.
  • organize citations and sync with webserver
  • excellent search capabilities
  • in-built pdf viewer
  • can generate (and keep it up-to-date) bibtex entries of all citations or per collection
• Papers2
  • for Mac & Windows
  • seamless integration with other programs (add citations to Word documents, emails, etc)
  • great management of articles
  • PDF annotation (highlighting, comments), PDF viewer
  • brilliant meta-data extraction and automatic annotation
  • not free, but there's an academic discount

You can find comparison of citation managers on wikipedia.

If you want to get bibtex entries directly from pubmed, use this to query:
http://www.bioinformatics.org/texmed/cgi-bin/query.cgi