Just watched this video showing how one guy keeps his references organized. It's included below, and worth watching. My own citation organization isn't as clean, but uses basically these same tools. (Read that as: this is how I should do it!)
I'll also note that I'm a bit conflicted about whether to use BibDesk to organize my files. The definite pros are that I'm already using it to organize my references and that it is free. I've been using Yep! to organize my documents, which don't always need to be in my bibtex library, and it is a pretty nice application. The downside is that it isn't free (I got it in one of those bundles). I think Yep! is very similar to another application called Papers that I know some people like a lot.