Western cartoons that did well in Japan?

Transformers, definitely. They even continued the story past season 3 with 4 more series (headmasters, masterforce, victory, and zone), as well as manga series, 2 cel-animated versions of beast wars, and much more. Heck, until TF:A in 2007-8, all TF series that were airing in America after beast machines (Robots in Disguise,Armada,Energon,Cybertron) were Japanese imports.
 
No there pretty popular especailly the X-Men they loved the 90's series probraly the most. The capcom fighting game was pretty much based on that version. I have no idea about X-Men Evolution I dont think it was never seem to find fan artwork or doujinshi based off that version at least not as much as the other versions (90's, capcom game, comics, and movie).

Also Teenage Mutant Ninja Turtles was pretty huge in Japan during the 80's it even got two OVA's lots of manga adaptations and some original stories. The 2K3 series was pretty well recieved as well.
 
There were japanese TMNT 2k3 fansites before the show aired in Japan. yeah that sort of thing is common in America for fansubbed anime. In happens in japan too.
 
Tiny Toons, Disney, Peanuts, basically they've all been named.

didnt know Animaniacs did so poorly in Japan, guess it didnt have the "cute animal" traits that Tiny Toons did...
 
Wow, Western toon subbing. I wanna see that one.

And yeah, I think specific American comic book superheroes are popular in Japan (e.g. Spider-Man and Batman), after all, the idea of Henshin heroes did come from them.
 
Gargoyles starting airing on the Jetix block of the Japanese Toon Disney channel around 2005. All episodes aired, even the Goliath Chronicles.
 
Aside from the ones already mentioned, Spongebob is pretty popular (an understatement, I'm sure) in Japan, going back to the whole cute look (Where isn't he popular?)

At one time, Ren & Stimpy (and Spumco in general) was popular, and Zim (so I heard) had a small following.
 
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