I recently got my hands on both the floppy and CD versions of Cryo's original Dune game, and I noticed the vast differences. Besides the introduction of voiceovers and clips from the David Lynch movie, they also replaced large swaths of the game, such as the travel animation and the sietches with pre-rendered 3D. At least they had the good sense to leave the music alone.

I was wondering what other games have such large differences between the two versions, especially considering that some of these games might eventually see release on GOG.

Corridor 7 had several differences between its floppy and CD versions. Hopefully that'll make it here someday.

The CD version added 10 levels, multi-player, an extra difficulty level, and (I think) CD audio.

I think there are also differing floppy and CD versions of Operation Bodycount.

Jazz Jackrabbit was both on floppy disks and CD, with the CD version being superior with improved music, extra levels, animated cutscenes etc

TES: Arena also was initially on floppies but later there came a CD version that had some extra stuff like a fancy into at the start

first ones that come to mind

I know that the CD version of Wizardry 7 had improved mouse and sound/music support, but it also didn't come with a game manual... so for the copy protection ("What's the word on page X, paragraph Y, word Z?"), they just gave you a .txt file with the passwords. Unfortunately several passwords were missing and others were incorrect, so there was about a 10% chance you had to restart the program, which was kinda irritating. A correct password list was eventually compiled, thanks to the internet.

I don't understand what was the point about Wizardry Gold.
The voice acting was painfully bad; easily the worst I've ever heard in a professional game. Even most amateur efforts for various mods are better.
The diplomacy was broken.
The new "improved" character portraits looked like some childish anime crap.

Star Trek 25th Anniversary and Judgmental Rights both have the original casts doing voices in-game on the CD editions that are missing from the floppy editions. There are probably other differences, but I haven't played either to know them.

I'm actually not even talking about Wizardry Gold. They made a CD version of the original game in 1993, a year after the initial floppy release. That's the version I have. Though I have played (briefly) WizGold and agree completely with all of your points. Almost all of the changes made it a worse game, except for a couple of technical ones. It had Windows support, and it didn't have the divide overflow bug that would cause errors on systems faster than about a Pentium 120. Since the dawn of DOSBox, there's been no reason to play Gold whatsoever.

If i recall correctly Dungeon Keeper has different floppy and CD versions.

Ah...didn't know there were three different versions. Thanks for clarifying.
I just finished the DOS version. Of all the old school CRPGs I've played it is the longest.

Oh man, loads of games. When you think about all the adventure games that had voice acting added and all the added videos, you're not talking about a small list of games.

System Shock - Shodan apparently had a voice in the CD version, but that's not the version I own.

There were actually plenty of differences.
-Voice acting was only in the Cd-rom version
-CD-rom version supported higher resolutions
-Most cutscenes had fewer frames of animation in the floppy version, and the death animation was very different in the CD-rom version
-Some levels had some minor added content in the CD-version.

I remember Menzoberranzan and Ravenloft series have differences between floppy and CD versions. Nothing major though, just some missing playable characters or something like that.

Indeed, I can't recall any FD based game using more than about a dozen disks. So, we're talking about games that are at most 30mb or so, and even one of those tiny promotional CDs holds 4x as much data.

Very few games that were ever released on CDROM were exactly the same as the FD version, because people expected to get more for their purchase. CDROM games cost more early on and were usually promoted as being premium content.