That's rough because for many of us, the NES practically was our childhood. Meanwhile Sega (very)quietly released the Master System into a market the NES owned. I personally didn't even know the Master System existed until emulation existed.
This guy has his opinion on some:
http://www.retro-sanctuary.com/Comparisons%20Main.html
A quote from Barone at Sega-16:
"
Cross platform games which show Genesis/Mega Drive strengths over the SNES* (
it doesn't mean the Genesis versions are superior in every way)
Aero the Acro-bat and Zero: The Kamikaze Squirrel games - SNES versions have the gameplay hurt by the cropped/narrower view due to the lower resolution.
Battletoads & Double Dragon - Bio screens simplified and cut scenes using smaller/recycle sprites on the SNES; more background animation on the Genesis; same cartridge size (8 Mbit).
Link 1:
http://www.gamepilgrimage.com/conten...sis-comparison
Link 2:
http://www.youtube.com/watch?v=wOjViZaaLrQ
Cool Spot - Wrong aspect ratio in the SNES version graphics due to the lack of 320x224 screen res support, some animation cuts, missing a few music tracks and some smaller background objects when compared to the Genesis/Mega Drive version using the very same cartridge size (8 Mbit).
Link:
http://retro-sanctuary.com/Comparisons-Cool-Spot.html
Demolition Man - Cropped view due to lower resolution, with more slowdown and noticeably inferior sfx quality on the SNES.
Link:
http://www.youtube.com/watch?v=IbSwEprjE0E
Earthworm Jim - Wrong aspect ratio in the SNES version graphics due to the lack of 320x224 screen res support, a whole level is missing, missing/recycling sfx and some animation cuts when compared to the Genesis/Mega Drive version using the very same cartridge size (24 Mbit).
Link:
http://www.retro-sanctuary.com/compa...orm%20jim.html
Flashback - Plagued with slowdown and loading pauses on the SNES; also lack some sfx and music tracks while using a bigger cart (16 Mbit) than the Genesis/Mega Drive version (12 Mbit). Link:
http://youtu.be/2B-F59VNbrw?t=28m
International Superstar Soccer - A lot of slowdown on the SNES in the most intense moments while trying to score a goal (when there's a lot of players appearing on the screen at the same time).
James Pond II: Robocod - Tons of slowdown on the SNES.
Joe & Mac - Tons of content missing (moves, enemies, levels, animation frames) on the SNES using the very same cartridge size (8 Mbit).
Link:
http://www.retro-sanctuary.com/compa...and%20Mac.html
Kawasaki Superbike Challenge - Only the Genesis/Mega Drive version is polygonal (with very good frame rate for the time and hardware) and a lot better looking than the SNES version.
Link:
http://www.youtube.com/watch?v=4j5HinyVHgM
Mickey Mania - More levels and no loading pauses prior to the stages like on the SNES while using the very same cartridge size (16 Mbit).
Micro Machines 2 - Reduced sprites for the cars in the selection screens and a few animation frames missing on the SNES when compared to the Genesis/Mega Drive version using the very same cartridge size (8 Mbit).
Link:
http://www.retro-sanctuary.com/Compa...achines-2.html
Mortal Kombat II - SNES version runs in permanent slowdown, lower resolution and has far worse characters' idle animation.
Mortal Kombat 3 - SNES version runs in permanent slowdown, lower resolution (with background art being changed/reduced to fit the screen and thus looking a bit different from the original arcade game) always noticeably slower than the Genesis version - which slowdowns only during combos.
Mr. Nutz - No loading pauses prior to the stages like on the SNES while using the very same cartridge size (8 Mbit).
NHL series from EA - Far better frame rate on the Genesis/Mega Drive.
Out Of This World - Plagued with slowdown and loading pauses on the SNES.
Outlander - Far less slowdown on the Genesis/Mega Drive during the driving segments.
PGA Tour series - Far shorter loading times on the Genesis/Mega Drive.
Phantom 2040 - Animated clouds and no in game loading pauses like on the SNES using the very same cartridge size (16 Mbit).
Populous - Far better frame rate on the Genesis/Mega Drive.
Race Drivin' - A lot more slowdown on the SNES.
Raiden Trad - The number of enemies' bullets was reduced on the SNES version and it still has a lot more slowdown than the Genesis/Mega Drive version.
Samurai Shodown - Far bigger sprites on the Genesis/Mega Drive version, with far better sfx quality. Link:
http://www.youtube.com/watch?v=M4ENYmSzxZY
Side Pocket - Slowdowns on the SNES with none of its music tracks matching the quality of the jazz stylized drums of the Genesis/Mega Drive version.
Link 1:
http://www.youtube.com/watch?v=b3p3-...DEC3FE4AD32257
Link 2:
http://www.youtube.com/watch?v=KnVYE...D0F0172E1E3BF1
Strike series - Far better frame rate on the Genesis/Mega Drive with higher screen resolution.
The Chaos Engine - A lot less slowdown on the Genesis/Mega Drive with higher screen resolution.
The Lion King - Cropped screen in the SNES version due to the lack of 320x224 screen res support and some animation cuts when compared to the Genesis/Mega Drive version using the very same cartridge size (24 Mbit).
The Lost Vikings - Higher resolution and five extra levels on the Genesis/Mega Drive using the very same cartridge size (8 Mbit).
Thunder Force III - A lot of slowdown on the SNES.
Toy Story - Lower resolution with cropped image view on the SNES, animation cuts, a whole level missing and Pizza Planet level with bad frame rate and only drawing a small portion of the screen, while on the Genesis/Mega Drive it's faster and fullscreen using the very same cartridge size (32 Mbit).
Link 1:
http://youtu.be/p5L-YtrQg5k?t=11m8s
Link 2:
http://youtu.be/p5L-YtrQg5k?t=19m39s
Ultimate Mortal Kombat 3 - SNES version runs in permanent slowdown, lower resolution (with background art being changed/reduced to fit the screen and thus looking a bit different from the original arcade game) always noticeably slower than the Genesis version - which slowdowns only during combos.
WWF Wrestlemania: The Arcade Game - SNES version has far worse frame rate and allows only three wrestlers on screen against four on the Genesis/Mega Drive. SNES version also can't play different voice/commentary samples as quick as the Genesis/Mega Drive version which is far closer to the arcade.
*All gameplay videos linked were recorded from real hardware AFAIK."
Again, as his note at the beginning states, that doesn't necessarily mean the Genesis version is better, but that is what those versions do better than their SNES counterpart. If someone does want to take a good look at them, there's something to be on the lookout for.