My favorite is Macross: Scrambled Valkyrie. Even the "colors are for fagorts" MD/PCE fanboys usually respect this one. IMO the graphics are basically unequalled in 16-bit home consoles, except for maybe Pulstar. The sound is pretty great too. Gameplay is about B grade, probably too easy for a lot of people.
I don't have any explanation for how this game turned out so good. Most 16-bit anime licensed games aren't even playable, let alone good.