Wario Land 3. Very ambitious for a GBC games, weird and unique progression and clever level design. Often overlooked due to the admittedly beautiful Wario Land 4 which is also easier to pick up and play.
If we count Nintendo published games: Sin and Punishment Star Successor or Last Window: The secret of Cape West. Both near flawless but niche games, playing to their respective consoles' strengths.
EDIT: Oh, Mario Golf Advance Tour on the GBA was also such a weird standout. All mario sports games are at least decent but Camelot pulled something special with that one.







