Clock Town for sure. Skyloft, Windfall, and Hyrule Town (Minish Cap) were all pretty great as well.
Skyloft/Windfall Island
Clock Town may have the most to do, but nothing beats chillin' in the skies with Skyloftians or flying around Windfall with my Deku Leaf. The aesthetic approach has a lot to do with it too. Staring out at the expansive sea/sky always gave a me a home-y feeling. I don't know how to explain it, but whenever I walk around these towns I could just stay there forever.