Windfall Island. Windfall is massive and filled with sidequest. The island is filled with shortcuts and interesting characters who wander about. The night auctions and thievery add character to the fascinating town.
Kakariko in Oot. Liked the music.
Clock Town in MM. Liked the sections and everything to do
Outset in WW. Just liked the people on the island better.
Ordon Village in TP. Liked how it was just a quiet little village.
Skyloft in SS. It's the only town in Skyward Sword!
I'll pick a favorite from all the games I've played.
Phantom Hourglass: Anouki Village( Isle of Frost)- This choice is mostly because of the fact that I love the Anouki race. They are so cute and so informal. Dee Ess Island and the Uncharted Isle were favorites from there too (though I suppose they aren't truly villages.)
Spirit Tracks: I haven't played Ina while but I like Papuchia Village for its name. The fact that there is mostly women there reminds me of the Gerudos. The Anouki Village is another favorite for the same reason above.
Ocarina of Time: This is a tough one, but I think I'll have to say Kakariko Village. I like how it is the place for both the living and the dead. The Gerudos Fortress is a close second,though.
Twilight Princess: It's a tie between Castle Town and zora's Domain. Castle town is the best one out of all the ones I've seen since they really nailed the city air. Zora's Domain was extremely peaceful as well in this particular game.
Im going to be completely honest here. I like Lon-Lon ranch from OoT. =D I LOVE horses and everyone who raises them, also it was a pivotal point in the story of the actual game. Anyway, That ranch wins my vote.
Hyrule castle town. from all of the games. It's just so lively and bustling with life, amazing <3
Ohh, but I loved Zora's Domain in TP ^___^ So preeettyyyyy.
Either clock town or Kakariko (All games that its in). Both have cool music and Clock Town had so many things to do. Castle town from TP wasn't as good as Clock town because there was close to nothing to do.
I like Karikio village in oot. I love the windmill and the graveyard in it. The place seems so lax and nice. It is the gate to 4 temples- Fire T, Shadow T, Well, Dong Cave. There are just so many reasons.