I haven't read every comment but ill just give my list:
Arcade
Street Fighter III. firstly the pixel art and just art in general is very good, but what sets this game apart from every other one is the animation. This was the game that practically started clothing animation. It does everything perfect, smears, anticipation, smooth in and out etc. When you need to make a fighting game, just look at these animations. (Skullgirls actually did this)
Red Earth. My favorite looking arcade fighter, it's just so pretty, especially the colours.
Darkstalkers/Vampire franchise: these also just have amazing art.
GBA:
Minish Cap, just wow. this is Sel-out heaven. the only problem with the art is that its meant to be seen on a gba screen, so if you see it on a normal monitor it looks way too saturated.
Pokemon R/S/E: This is imo the pokemon game with the best sprites. These even look nice on a normal monitor. The spritework is just top-notch.
Golden Sun 1 and 2: Even though these were just 3D models made into sprites, DKC-wise, this game still looks amazing and aged a lot better than DKC and Super Mario RPG.
Misc.
Breath of Fire IV. I rarely see any praise for this game, but damn this is something. Maybe it's rotoscoped, i don't know but the art looks amazing.
Star Ocean Blue Sphere. This game may not look that amazing to the untrained eye, but this is as good as it gets on the GBC.
