I'd have to say the fishing hole, but it's really hard to decide. One of my favorite things about Twilight Princess was the landscape, and I personally think it has the best over world in the series.
The City in the Sky, Zora's Domain, and Gerudo Desert were my favorite aesthetically. Each had its own style that felt like it had some genuine effort and feeling, and they were all so pretty
I'm a fan of Ordon Ranch. Sure, it's kind of empty, but the view of the mountains is nice and the music is very calming. Also, its about the only place in the game that never has any enemies or bad things happening, which makes it feel very safe.
My second choice is the Forest Temple. It has some very nice rooms that seemed really wild, but very bright. The boss room after Diababa is gone looks really serene.
The City in the Sky was, and still is, my favorite dungeon of any zelda game I've ever played. And there are seven of those(but I've only beaten five of them), so I'd choose the City in the Sky. Or the Twilight Realm. But mainly somewhere with a good view of the sky. I've always thought of those types of places as having their own unique, serene beauty.
My favourite place was Zora's Dominan/Fountain place. (it's been awhile since I played this game so I apologize for making a mistake in the name)
The waterfall was breathtaking. I enjoy waterfalls like that and especially the Queen's, (Prince's) Chamber is gorgeous.
If I would grow gill's I would join the Zora's Community.
The Sacred Grove was a beautiful place, including the nice music that went with it (along with the revamped Temple of Time). I also loved the fishing area; the trees and waters created the most dazzling atmosphere. Though I think anything touched by the sun or moon of this came was fantastic, I think these would be my favorite two.
Sacred Grove is the most beautiful place to me, it just reminds me so much of OoT. Not to mention the forests actually look real if you don't look too hard at them.
I pretty much loved all the areas in TP, but there are a few that really stand out for me.
The inside of the Temple of Time. The dungeon might have suffered from a lazy layout, but I loved the ancient atmosphere and how bright most of it was.
The fishing pond. That area is just so relaxing and the changing seasons was a nice touch.
Castle Town. I didn't really mind that you couldn't talk to most of the people, I just liked the layout and it felt more like a city to me than the one in OoT.
I'd have to say the Gerudo Desert and the Sacred Grove. Also the room that you defeat the boss of the Forest Temple in, when it's cleared out is really pretty.
Fishing hole for the natural beauty category and overall, The Temple of Time interior for architectural, The Sacred Grove for historical, The City in the Sky for mechanical/fantastic.