Kanto is an actual region in Japan; I've heard references to "the Kanto prefecture" more than once. And the others, while not named the same as any particular place, can generally be correlated to some Japanese area.
EDIT: Here you go.
Johto lies directly to the west of Kanto, to the northeast of Hoenn, and is based on the Kansai region of Japan.
Hoenn is roughly based on Kyūshū in Japan (flipped by 90 degrees and smaller, possibly influenced by the Shikoku region as well) and lies to the southwest of Kanto and Johto in the Pokémon world.
[Sinnoh] is based on the geography of the Japanese island of Hokkaidō, the southern end of the Russian island of Sakhalin, and the disputed island of Kunashir.
According to Pokemon.com, [Orre] is based on the Arizona desert, although the game has a post-apocalyptic feel to it as well.
Hooray for Wikipedia.