We had a fun little session on research tools this morning. I spoke about Yep, a PDF management app for the Mac. I’ve been playing with it for a while, and I can recommend it, although it lacks a social network interactive folksonomised video web 2.0 interface 
Ismael has a list of the tools. I particularly like Dapper.net for graphing/analysing and generally playing with data.
You might also like Skim – its a PDF reader with annotation:
http://michael-mccracken.net/wp/2007/04/02/announcing-skim-stop-printing-start-skimming/