I'm currently using Together, and I really like it. Prior to Together I was using Eagle Filer, and I liked that too, but I was frustrated by its lack of smart folders.

Together has the same approach as Eagle Filer, its stores its files inside your Documents folder, so its non-proprietary. Not only does that make things easier down the road, it means it takes all files as is.

I also like its tagging features, and it can now sync with .mac.

I've tried Yojimbo and Devonthink briefly, but they never really worked for me.

Basically, I throw everything in there, spreadsheets, pdf's, mind-maps, scanned files, and stuff I've written. I go through and tag them if there's time or just use search through it for the file I need when I need it.

What I've found with these "store everything" apps is you really have to find the right one for you. If you haven't yet, give Together a try.