It's hard to choose, I love all the areas pretty much lol.
Lake Hylia is always fun in whatever game it's in, there is always lots to do around it. As is the Lost Woods or any forest environment. As mentioned earlier Ikana Canyon is really one of the best places in the series too, a fascinating region.
Kakariko is also one of the best places in the series, but I really don't like it in TP. They made it seem like an old west kind of town, and Kakariko just isn't that kind of place imo. To me anyways.