Lemmings had a special CD version release later that had full RedBook audio. A godsend for PC gamers that don't want to emulate the Amiga version or put up with the absolutely dreadful MIDI music. The CD had the full theme for the SOTB-inspired "A Beast of a Level" stage, which made it worth putting into a hi-fi and playing full blast...
Didn't the latter two Ishar games have special CD versions with prerendered intros and Redbook as well? I think I recall both versions being in the GOG releases, but I'm too lazy to check...
SCPM: Flashback: Quest For Identity had very different cutscenes between the two versions. In my opinion, the CD version was worse. I forget what the other differences were.
Agreed. Not only was the MIDI music actually better, the prerendered cutscenes look horrible.
As I recall though, you can use REminiscence with the files from the CD version to play the floppy version, or even download the Amiga music MOD files and have the all-round best experience (nothing beats the awesome Amiga version).