Phew, and I thought this was going to be another hardware vs thread like we've had so many times in the past. This is better

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Air Buster/Aero Blaster – Not sure, really about equal to me. I'd probably prefer the PCE one though if I went back to compare.
After Burner II - PCE
Atomic Robo Kid – Are Atomic Robo Kid (MD) and Atomic Robo Kid Special (PCE) different games or what? I haven't played both enough to see if they have the same levels and stuff, but they always seemed different to me. I'd probably give Genesis the upper hand on this since I remember really liking that version, but I like Special too.
Forgotten Worlds - Another tough call since I've barely played the PCE one. Graphics and sound are no doubt better in the PCE one, but it's lack of true two-player support hurts it in my opinion. I'll give it equals for now.
Raiden - PCE easily.
Winds of Thunder/Lords of Thunder - PCE easily.
Snatcher CDROMantic - Well I think the PCE one is a better game overall, but since I don't know Japanese, it brings it down some notches (though I was still able to understand it pretty well since I beat the Sega CD one before). I'll give the hand to Sega CD since understanding the story is more important, but PCE would win if it was A. ) In English, B. ) If I knew Japanese

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Street Fighter II' Champions Edition - There's just some really appealing about that thick HuCard for the PCE one

. I prefer the PCE one overall for it's sharper graphics and sound (for the most part). To give the Genesis one credit, it did have that extra "KoF-style" mode, but I never use that mode anyways since it's not true three-on-three gameplay. It also had that cooler opening with the street fight.
Fatal Fury 2 - PCE easily. All SNK fighter ports are better on PCE

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Fatal Fury Special - PCE.
Art of Fighting - PCE.
Cadash - PCE easily.
Daimakaimura (Ghouls 'N Ghosts) - Super Grafx. Never really found anything better about the Genesis version, except the fact that it made the console more appealing for it's time.
Golden Axe - Never played the PCE one, but I think it goes without saying that the Genesis one is better!
Juuohki (Altered Beast) - Genesis easily. Graphically I do prefer the PCE one, but the sound effects and better controls make the Genesis version an easy win

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Shadow of the Beast – PCE easily, for the music reason Tat stated.
Valis III – PCE. Music wise is up for debate, but the lack of levels in the Genesis version is the killer. PCE also had tigher graphics and cinemas.
Wonder Boy III: Monster Lair - PCE easily. Genesis verson was a dithered mess and the sound just couldn't compare to futuristic CD technology!
Wonder Boy in Monster World/Dynastic Hero - Very close, but I do prefer the PCE overall for the little better color and music (plus opening cinema).
Dragon Slayer: The Legend of Heroes – I'm not sure why Tat preferred the MD version, but I definitely prefer the Turbo version much more. Way better music and graphics (I prefer the cutesy colorful graphics, over bigger darker graphics), plus it had, albeit few, awesome cinemas.
Dragon Slayer: The Legend of Heroes II – I never really played much of either, but it seems to be the same case scenario as the first DS game.
Exile – PCE definitely.
Popful Mail – A true ball buster decision! I vote them equally because they both have their own qualities.
Ys III – PCE in my opinion. The crappy parallax does hurt the PCE pretty significantly, but overall I prefer the PCE version much more. Check out my comparison
here for more info (SNES verson included too).
Bomberman '94/Mega Bomberman - PCE easily.
Columns – Ehh, haven't really compared. I'll just say equal.
Devil Crush – PCE overall for me.
Dodge Danpei – I don't really think this is a fair comparison as they are different games from what I remember. Either way, the PCE game was way cooler and more fun.
Outrun – PCE overall, I liked the graphics more.
I've always thought that PCE had better ports in general.