I ripped my entire CD collection to MP3 (about 12 gig worth) a few years ago when I bought a first gen ipod mini. I bought a bunch of music through itunes for a couple of years, but now Amazon.com has a ton of stuff for the same or cheaper price as itunes, but the Amazon.com music is DRM-free so you don't have to worry about license authentication or anything like that.
I'd first rip your existing music collection, and then fill in the gaps from amazon.com. Whatever you still can't find, get from itunes but immediately burn it to CD and re-rip to DRM-free MP3 so you never lose your ability to play the music if your licenses get messed up.
There are other independent music repositories out there but my taste in music isn't very experimental so I haven't gone looking for any indie bands to listen to.