I always found the uniformity of the grid pattern in SMS boxes to be so boring. Then the art used was so blah. I can only recall Ys, Phantasy Star, Miracle Warriors, Golvellius, RType and Aztec Adventure being pleasing. I remember actually buying Ys just because of the box art (and because I had just gotten done with Phantasy Star and wanted more of the same).
I was always envious of the diversity found in NES boxes, where each publisher had their own style. Sure, they were missing the awesome clamshells, but the art was generally more colorful and interesting.
I also must be part of the 0.1% that actually likes the Dungeon Explorer USA art. I like the colors used and the sort of impressionist approach taken. It gives me the feeling of going on an adventure in some fantastic land, and actually prefer it to the PCE version (although that one is nice too).
In general, I would say that the worst cover art comes from SMS and the Turbo, which as stated earlier, seems odd, since Atari, Intellivision, Coleco, Odyssey, etc. covers were usually very well done.