Hmmm... things might have changed since I was there in '03, but I remember these stores in particular having good CD selections:
MK: County Bounty (in Toontown), Main Street Cinema, Mickey's Star Traders
Epcot: Mouse Gear
Studios: Can't think of any really good ones right offhand...
DAK: Can't remember the name of it, but it's the one near the entrance to the Pangani Forest Exploration trail - this one at least had the Animal Kingdom-oriented CDs, which is about as good as I remember it getting at DAK
Downtown Disney: World of Disney (usually carries most, if not all, current park CDs)