If you're an audiophile, I'd suggest going with the single disk CD player. Less chance of foul ups due to mechanical complexity. Multi-CD machines, especially the ones that hold 100 or more means greater complexity. (Of course, some folks would say that only true audiophiles listen to LP's, but then that's another story.)
More complexity=greater chance for FU's.
If you're not so much an audiophile, and want music in the background and greater convenience, having music loaded on a computer/Ipod/MP3 player and played through your sound system is the way to go. Easy access to songs by title, or artist, and way more convenient compared to any multi-CD changer.
Another option is to create your own mixes of MP3's on recordable CD's that can be played back on a compatible CD player.