I'm only counting games I have played on those systems, actually.
NES: Super Mario Bros. 3
SNES: Yoshi's Island
N64: Banjo-Kazooie
GCN: Metroid Prime
Wii: Super Mario Galaxy 2
Wii U: Pikmin 3
GB: Zelda Link's Awakening
GBC: Zelda Oracle of Ages
GBA: Wario Land 4? Hard to say here, GBA has a lot of very good games, but none that stand out completely to me as the best.
NDS: Yoshi's Island DS
3DS: Super Mario 3D Land
Switch: Mario + Rabbids Kingdom Battle (will verey likely change when Mario arrives ;))
SMS: Sonic Chaos
GG: Sonic Triple Trouble
SMD: Sonic 2
Sat: NiGHTS into Dreams
DC: Sonic Adventure 2
XB: Super Monkey Ball Deluxe
360: Sonic Unleashed
Bone: Yooka-Laylee
PS1: TearRing Saga
PS2: Jak & Daxter
PSP: LocoRoco
PSV: Super Monkey Ball Banana Splitz
NGPC: Sonic the Hedgehog Pocket Adventure
VB: Wario Land VB
PC: Commander Keen 4
EDIT: I also have a CD-i, but no games for it, so not listed.