I think much of this has already been said, I would add a few things.

I used to be a big fan of Devon think and will probably go back to using them. If you decide to give it a shot, I think there's a lot of reason to use it in it's indexing capacity, which makes it more like a finder replacement/competitor that lets you keep a handle on what you're working on, but it keeps you free.

I definitely think that Eagle Filer is probably one of the best apps in this space though, it's all open (ie, it' just acts as a layer on top of your files, rather than a storage format), and is pretty good in this space. I don't have a lot of direct experience with it.

Yojimbo is also great, but the fact that you can cascade folders always annoyed me a bit. You can't beat it for easy capture. Well, truthfully, there are ways to script easy capture in any of these systems, but it's simple and pretty in Yojimbo.

Frankly, however, these days, for all my PDFs I use BibDesk to maintain a bibTeX file. This only really works if you use LaTeX/bibTeX, which you should ;), and I just have all the files labeled with the cite-key. Spotlight still works, and I have a program that will keep track of things, a file format that's plain text/human readable/editable.

For the files I edit and work with on a daily basis I have a local subversion repository (that I sync up off site), which is good for keeping things mobile and able to keep track of versions without needing to pay attention to partiuclar instances of files. It's a good system.

This might all be more geeky and elbows deep than you want to get at this point, but it works for me.

Cheers,
tycho