Whew~ Man, what a thread! Twilight Princess features the best locations in the whole series. Choosing an answer is gonna be hard...
Lake Hylia, Zora's Domain and Snowpeak are great answers! I just wish there was more to Snowpeak. Snowpeak Ruins is an awesome location.
Eldin Field is impressive, lying there beneath the imposing caldera of Death Mountain with its astounding panoramic view, massive crevasses, distant wooded field, mysterious ruins and of course the majestic Eldin Bridge. It also features a surreal view of Hyrule Castle encased in its golden barrier. A nice little touch I always admired was the solitary mine shaft in the distant inaccessible cliffs across the crevas that delves into the bowls of Death Mountain. It lends a sense of interconnectedness between the lands of Hyrule that is woefully absent from much of the series but that is very prevalent in Twilight Princess.
But if I had to pick one location, it would have to be the forest. It is a lost otherworldly place seeped in atmosphere. Just being there, anyone can get the feeling of some sort of connection to a long forgotten past. Being there feels like standing all alone on the edge of time itself. Somehow, the forest seems steeped in Hyrule's history. And, of course, it is the forgotten resting place of the legendary Temple of Time and the Blade of Evil's Bane. The furthest reaches of the forest, the Lost Woods and Temple of Time feel like no other being - save for the enigmatic Skull Kid - has tread foot there in ages.
It is a mystical, alien local that at the same time feels uncannily familiar.