I mentioned before that Mendeley was out and appeared great. After reading comments on it from another PhD students and faculty I am now wishing I had the time to move over to it. I may do it yet… (AFTER I defend my proposal November 9th).
In the meantime, if you are curious about how to use a tool that catalogs pdfs, inserts citations and allows you to take notes all in one interface, check out these articles:
SXSWi discussion: Mendeley
Using Mendeley for Research Management
Using Mendeley to Manage Readings and Citations
Another reason I love Mendeley: Grading student projects!
If I decide to convert after the proposal review, I’ll write up my process.
ProtoScholar 
I use Mendeley and it was actually easy to switch to. I love that it will use Google Scholar to try find the information for any pdf it loads as well as organizing into folders the pdfs in your collection (think iTunes). I would strongly suggest it to anyone that has more then ten or twenty papers to keep track of.
Thank you for the link over to Mendeley…I’ve not heard of it before now and I think I will switch over. I’m early enough in my research to do so
Thanks for linking! I hope you have time to “take the plunge” after your defense – as you can tell from my posts, it has been very useful to me, including in ways that the Mendeley team hadn’t thought about! And there are still tools that I’m not taking advantage of, too.
Doesn’t it not work with Mac Word?
I had thought it was completely cross platform, but since I don’t have a mac i’m not sure. Does anyone know the answer?