I've got too many, wouldn't know what order to rate them in at all.
SNES: Lufia II, Super Mario World: Yoshi's Island
N64: Ocarina of Time/Majora's Mask
GBC: Pokemon R/B/Y/G/S
PC: Half-Life (+2 and the episodes), Warcraft III, Age of Empires 2
I could list more but these are definitely all in my top bunch easily. If I had to pick two, it'd be Half-Life 2 and Ocarina of Time