I use JabRef as my preferred bibliographic management system. It's aimed at BibTeX and it uses it natively (the database(s) is just a regular BibTeX file). JabRef is (being) developed in Java so you can use it in Windows, Linux, Mac OS...
It supports (imports) a lot of bibliographic formats, such as BibTex, RIS, Endnote, just to name a few.
It can fetch citations directly from Citeseer and IEEExplore (and other services, but these are the ones I use most).