I haven't used it personally but have heard only good things about songbird.
I don't let iTunes do anything other than act as an interface for my iPod. It doesn't manage my music and I don't use the iTunes store. I even manually load my podcasts through their respective RSS feeds.
MediaMonkey is a good application and comparable to iTunes. Takes a bit of customization to setup for use with an iPod but I think it does a great job. Songbird as mentioned above is a nice tool also.