I really like the Zoras in Twilight Princess, and I know that they don't really live in a town, but I choose the Zora Village for my #1. In second is definitly Kakariko Village in Ocarina of Time. It is very rural and is at the base of the greatest mountain in Hyrule. 3rd is the Hidden Village in Twilight Princess, because Impaz governs a town full of cats (I know, I'm just wierd).