As Karateka was mentioned already, I'll say Prince of Persia.
Yes, there is a SCD port of this game, and it's not a bad one, but I think some aspects of it are a bit off. Some of these are possibly related to the later enhancements, but anyway:
1. It seems that there aren't as many frames as in the original versions, making the movements a bit stiff.
2. I personally don't like the speed setting(I think this was an additional feature originally introduced in the Japanese computer ports). IMO as the characters were originally rotoscoped they should only be played at one single speed to get the correct frame rate and smooth movement. While setting it to fast speed help you play the game in faster pace it just looks hilarious as hell, and even at the "default" (?) setting I still find it a bit off. Maybe this is one factor that causes problem 1 above.
3. The music cues and jingles. Personally I liked the original ones more. Granted that the original version didn't even have BGM played throughout and that the musics in the PCE version aren't bad, I still find the original ones more suited to the settings, even if you have to emulate how they're coming from Apple ]['s speaker (ideally it's even better if they're based on the PC DOS version, out of soundcards). When Mechner designed his games the presentations were very much related to film making, so the sounds of the original versions were carefully designed to make the game as cinematic as possible (same goes to Karateka).
4. The player's turban. It's also an addition originated from the Japanese computer ports I think. IMO the lack of this turban and the plain outfit of the player in the original versions made it more convincing that you're ripped off of your stuff and become a prisoner. I think even Mechner himself loved the changed though, so every subsequent ports had this change. This is not that important though.
Now that the original design documents and the source codes of the Apple ][ version are publicly available I think it is possible to do a PCE conversion to be as faithful as possible, and see how it compares to the SCD commercial release. It would be great if this version includes an option to switch between the original Apple graphics/sound and somewhat enhanced one too.