I have a few ties, but I narrowed it down as best I could :P
PC: (TIE) The Sims (original), Tropico 3.
NES: Super Mario Bros. 3
SMS: Alex Kidd in Miracle World
SNES: Donkey Kong Country 2: Diddy's Kong Quest
PS1: Tekken 3
N64: (TIE) Pokemon Snap, Paper Mario
DC: (TIE) Seaman, Crazy Taxi
Xbox: Wrestlemania 21 (The only game I owned for it, so not much competition :P)
PS2: The Sims: Bustin Out
NGC: (TIE) Pikmin 2, Paper Mario: The Thousand Year Door
Wii: (TIE) Captain Rainbow, Super Mario Galaxy 2
GB: Pokemon Green Version
GBC: Pokemon Yellow Version
GBA: Pokemon Ruby Version
DS: (TIE) Pokemon Black Version 2, Taiko no Tatsujin DS: Dororon! Yokai Daikessen!!
3DS: Super Mario 3D Land