Attention All You Graduate Students
One of my office-mates has just pointed out to me the most ingenious piece of software I've ever seen for organizing, reading, and annotating PDF files of academic papers: Mendeley. Seriously, check it out. It's even free!
It bills itself as being "like iTunes for research papers," and that description is quite accurate, even up to allowing you to assemble groups of papers into collections (playlists), copying all the files into a single organized directory, and automatically importing metadata (though that's a bit iffy on a lot of them). You can read, highlight, and annotate papers directly in the program. You can sort your entire collection by title, author, publication, keyword, etc. It can even search the body text of your entire collection for terms! (Well, as long as they're native PDF files rather than scans.) And possibly coolest of all, it stores up to 500 MB of your collection online for you to access from anywhere (and act as a library backup).
My only complaint is that it's a bit resource-intensive for my old laptop, which leads to some stability issues. But even with that, it's increased my research productivity immensely. I can't recommend Mendeley highly enough. Check it out!