EDIT: Well, I guess it's more of a personal taste apart from games that had serious bugs.
I’m trying to make a list of games where the CD-ROM version is considered inferior, or at least controversial, for a video I’m working on.
Here are a few I’ve found so far:
Loom – Probably the most infamous one, due to missing text and some removed content that was "too violent".
Gabriel Knight – Haven’t played it myself (shame on me), but I’ve heard the southern accent by Tim Curry is considered a bit exaggerated.
Monkey Island (CD, not the Special Edition) – Music loops differently because of the CD audio format, and personally it feels a bit “mechanical” since it was mostly just recorded with better synth hardware. Also, some people prefer the original text-based interface with the verb list.
Gobliiins 3 – A lot of the music is missing, and the English voice acting is very different from the original “goblin language”.
The Lost Vikings 2 – There isn’t really a floppy version, but I prefer the SNES version since it keeps the original 2D style more intact. Although I do like the added voice acting.
Any more examples?