Clock Town's great, and I really like how it feels so organic and real. You can tell effort was put into it.
But personally, I've always liked Kakariko Village from OoT. It's interesting how it changed during the 7 year gap. It goes from a relatively small, peaceful town near the Castle town, to the last places Hyrule survivors can go to. Not to mention the ruins of Castle Town are really just over the hill, and the Death Mountain looms over the village with it's flaming cloud ring.
I also like how peaceful the town generally is- it makes a sharp contrast to the Grave Yard, the Shadow Temple and the Bottom of the Well, which are all actually within the town.
Besides, I have fond memories of just playing around in Kakariko when I was bored as a kid. Haha roof hopping with the hookshot and flying around with that on Cucco inside the windmill.