FLCL - Image #816,489

Strangely enough, despite how good it is FLCL is practically unknown in Japan.

It's true, there are some occasions where an anime is not really big back in it's homeland, but is really popular to Westerners. Big O is another major example, as the show pretty much flopped in Japan, but when it aired on Adult Swim it was successful enough that Cartoon Network themselves provided funding for a second season (that I think only aired outside of Japan).

Same with some Japanese made games too. Aside from the Prime games (which are made in the US), the Metroid series was created in Japan, but has always been much more popular outside of Nippon. Zelda's been going this way for the past decade too, since to my knowledge no Zelda games after OoT have sold 1 million copies in Japan alone (Skyward Sword in particular, though it managed to reach about 3 million worldwide, only sold like 300,000 in Japan; I actually feel like maybe that's the real reason why Hyrule Warriors exists, to reignite interest in the series to Japanese gamers [since Warriors/Muso is huge over there]).