This reminds me of the ol' Sega vs Nintendo wars of the early 90's! Man, they were vicious.
I've owned both and have played virtually every game on both sytems (for the SNES, *literally* every game, even the indecipherable Japanese titles), and enjoyed them both a lot, but in the end I think it comes down to personal taste and neither is really "best." Just favorites. For example, I slightly preferred the SNES incarnations of Castlevania and Contra, and Konami's International Superstar Soccer on the SNES was always more fun than FIFA... but that's just me.
True, some of the great titles you mentioned were MD-only (except, Puyo Puyo 2 was on SNES, as was the Puyo 2 Remix!), but then on the flip-side of the coin are the SNES-only titles -- Mario Kart, Zelda 3, Super Mario World, Yoshi's Island, Starwing, Final Fantasy 3, Goemon, Super Metroid, Secret of Mana, and so on...
The best solution is -- HAVE BOTH, and enjoy the crap out of 'em!!!
@Killergorilla -- wow, what a Sega collection! Would love to have all those DC & Saturn titles...