Hmm, probably Hyrule Castle. While playing OoT, I fondly recall trying to find a way back in as a child after getting the Master Sword. Its music and dungeon is excellent in alttp. And TP's version isn't too bad either.
I like those as well. I also liked the amount of open freedom to ride Epona in Twilight Princess. It may have been mentioned before, but I always thought that Epona would look better with a more Medieval saddle rather than a Western looking one.
My favorite place in any Zelda game would have to be the very first dungeon. You get your first piece of equipment here as well as your first heart container and you defeat the very first boss! It's always so epic after you complete the dungeon for the very first time and you're like "OMFG. AWESOME. I LOVE ZELDA"
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.