For simplicity's sake, the NES generation will be called the first generation, and please do not say any PC or handheld games.
For me:
Generation 1 (NES) - Super Mario Bros
Generation 2 (SNES, Genesis, TG 16) - Super Mario World
Generation 3 (PS1, Saturn, N64, worst gen IMO) - The Legend of Zelda: Ocarina of Time
Generation 4 (Dreamcast, PS2, Xbox, GCN) - The Legend of Zelda: The Wind Waker
Generation 5 (360, PS3, Wii, oh and this is for "so far") - Super Mario Galaxy
Kinda weird how most of the games in my list came out within 3 years of the generation starting
Top 3 favorite games: Super Mario Galaxy, The Sims 2 (PC), The Legend of Zelda: The Wind Waker