I'm torn between Alien Soldier and Sin and Punishment for my favorite, they're their masterpieces, 2D and 3D respectively.
Mischief Makers is also genius.
Least favorite of the ones I played might be Light Crusader, although it's still pretty good, definitely feels the weirdest since Treasure didn't use to make isometric RPG-ish western-looking games, but it's not bad and it still has the Treasure feel here and there, oddly.