I am a research librarian (which means I actually undertake research projects for our staff at an economic development part of a university), so I do both academic and librarian work. I use PB to organize thoughts and references and Zotero, a free program specifically for academics, for storing papers and bibliographic references.
Zotero which is being developed at George Mason University, recognizes many article and bibliographic databases and grabs and organizes both the papers and the bibliographic information. It only works with Firefox, however. It has a great community of academic users. If I were just starting a big research project, I'd download this immediately.
In addition to text, it is set up to capture all kinds of information files - films, podcasts, interviews, letters, maps, radio broadcasts and much more.
I use mainly articles. Zotero aims to let you do what you can do with index cards and a reading pile - write directly on the article, add sticky notes, etc. It is a fabulous program for academics and serious researchers and it complements Personal Brain nicely.
It was one of 3 programs I focused on when doing a program on managing personal information at one of the huge library conferences last summer - the other 2 being Personal Brain and Evernote.
Less judgement, more curiosity