I dont mind the designs of the Neutron characters. On the other hand, the human characters in that Back to the Barnyard show scare the living crap out of me.
Dragonball Z is highest on my list. And yes, it has to be intentional because I know Akira Toriyama is more than capable of non-ugly thanks to Blue Dragon. I just can't stand looking at a thousand and one characters with their overly bulging muscles, half of which don't exist.
(Reminds me of that old engraving, "battle of the nudes".)
This isn't a cartoon exactly, but since video games are primarily animated, I have to say World of Warcraft. Every last character in that game has a malfoy-like sneer on their face. I realize some people might think it looks attractive and all, but to me, I can't bring myself to even think of playing the game...
Next on my list, Squirrel Boy and Gym Partner. I don't watch enough squirrel boy to really be able to state whether or not it works for the show, but Gym Partner seems to use the "ugly" factor to exaggerate how a certain monkey acts. I suppose that's successful.