NES - Only system I had at the time so it wins by default.
SNES/Genesis - Tied because I got pretty much equal playtime from both of them. SNES had awesome games like Super Mario World, Yoshi's Island, The Megaman X series, Killer Instinct and others while Genesis had the Sonic games, Phantasy Star, Herzog Zwei etc. Good times.
N64 - Playstation had far more games but very few approached the level of awesome that Nintendo's first party efforts reached. Mario 64, OOT, Star Fox 64, Mario Kart 64, Goldeneye, Perfect Dark, Majora's Mask, Turok & Turok 2 are all classics. Playstation had the greatest RPG line up in history though led by FFVII, Xenogears, FFTactics, and Chrono Cross but N64s line-up edges it out for me.
Playstation 2 - Without question the greatest console of all time. Pretty much has nearly every genre you could think of covered. Platformers, shooters, action games, fighting games, RPGs, PS2 has tons of quality games in all of them. It's RPG line-up is starting to rival even the PS1s with stuff like the Megaten games, Disgaea, Odin Sphere, Grim Grimoire etc.
Xbox 360/PS3 - It'll probably come down to those two although the Wii could surprise me. Right now the 360 and PS3 are tied in my book but the PS3 should pull ahead once MGS4 and FFXIII are released.