1) Exile. Try playing the Genesis version AFTER this one, or even worse, on the MSX2, and you'll see what I mean.
2) Lords of Thunder. The graphics still look better on the Turbo, and the lack of narration adds to the power of the music.
3) Emerald Dragon. I heard that the FM Towns version has all the music, and the SNES one has an English translation, but the voice acting and cut scenes of the Turbo are AWESOME!!!
4) Ys IV. I heard the SNES one is canon, but it's such a murky disappointment in comparison to the Turbo!
Okay, that's just a few. Feel free to add any others!