Well, this is a tough one.
The case for NES:
Mega Man 2 and 3: Two games which still has some of the best original soundtracks ever. Plus, they're fun to play if you've got an hour to waste.
Duck Hunt: I'm utterly amazed how the NES managed to put so much glee into a sound that really isn't like real laughter at all... But then again, perhaps it's like that Horse on the Chalk (if you're not a Terry Prathchett fan, you're missing out here), in that it's not what a malicously gleeful laughter sounds like, but what a maliciosly gleeful laughter actually is.
Rad Racer: Well, not really that good a car game, but again, some pretty cool scores.
Ninja Gaiden: The epitome of what a ninja game should be: Plenty of cool ninja tricks, a plot with death and betrayal, and of course, difficult as three hells, as -everything- wants to kill a ninja. (Which the ninja enjoys, because -he- wants to kill everything.)
The case for SNES:
Super Mario World: This is one of the few platform games that really stands the test of time. Some pretty damn accurate controls, lots of different stages, some corny humour, and so on... Probably one of the best launch games for any console.
Secret of Mana: It's strange that hardly any action-RPG hybrid still doesn't have much more reliable AI than this game (Heck, Tales of Symphonia is almost worse). And oh my god, some of the scores just grabs my spine and twists it. Especially the one in the snow area. How can something so simple make such a strong impression?
Zelda: A link to the Past: Yeah, can't get past this one. Unless you have heavy nostalgia factors built in, the first Zelda just doesn't withstand the stains of time as well as this one.
F-Zero and Mario Kart: Two racing games emphasising the fun in racing, in their own distinctive manners.
I don't know, it's a tough one. I guess the SNES wins out by a narrow margin...