Are you guys forgetting Zora's Domain from Twilight Princess? Oh man was that beautiful....especially at dawn where the mist made everything look hazy and glowy. Also Hyrule Field from Ocarina of Time 3D during the day and especially at night.
I've always loved Zora's Domain (since this is in the OoT section, I'm only gonna mention OoT locations), but Kakariko Village and Hyrule Market are good, too. And outside the Great Deku Tree is gorgeous