There are a few dj apps, but other than that, I don't know of any app which will manage your music library better than iTunes. winamp/winamp clones can't do that either, you work off folders. There are a few slightly more sophisticated players for Linux for instance, but all I know of (with one exception) are based on the actual folder structure (the last one is based on an SQL database, but is optimized for a touch screen interface).
Other than the DJ software, I think iTunes is still your best bet. You're more than welcome to try versiontracker.com.