This could take awhile, if I could even think of any so... So a few of mine will be things people have already, K?
SS Brawl > SS Melee, its easier to play and frankly has more
MK Wii> MK DD, game play is better and once again has more, level design, soundtrack. Oh yeah and regardless of how unfair it is to use bikes, its still fun.
SM Sunshine> Galaxies, better level design and G2 had what are possibly the worst bosses in the series, call me old fashioned but I prefer big well designed levels with a variety of challenge rather then next level, go through this path.
MK 64 sucked even for it's time, Diddy Kong Racing and crash nitro kart were way better. SSB (64) sucked even for it's time, the gameplay was meh but the concept was good
Zelda ST, PH and TP are great games, including touch screen controls
Pokemon Gold and Silver have the worst level curve and are the slowest paced of all pokemon games. (Still great and easily one of favs in the series)
Ill think of more (possibly ones that have not been said, but unlikely given how many posts there are) just give me a sec...
Please refer to me as 'Blake' it seems more personal without the G, thank you in advance.
I guess I need to provide my reasoning. Here are some of the games I consider great for each system.
SNES: Chrono Trigger, Earthbound, ALttP, Super Metroid, Super Castlevania IV, Super Mario World 1&2, Secret of Mana, Mega Man X, DK Country 2, FF VI, Super Mario RPG. Many franchises had some of their best games on this system.
GCN: Metroid Prime, F-Zero GX, Paper Mario TTYD, TWW, TP, Mario Kart DD, SSB Melee, Resi 4, Pikmin 2
Wii: Super Mario Galaxy 1&2, SS, Metroid Prime 3, DK Country Returns, Xenoblade Chronicles, SSB Brawl, Monster Hunter Tri
N64: Mario 64, OoT, MM, Paper Mario, Star Fox 64, Banjo-Kazooie
In my opinion, I think the NES is probably my favorite Nintendo system, though mostly for the historical reasons, as well as the large variety of quality games available for the system. Granted I do not own a SNES, so that may change when I get one.