It's technically more than one 'section,' but the period from the start of the Ancient Cistern until the end of the Pirate Shop dungeon in Skyward Sword are the best 8-10 hours of any game I've ever played. 2 masterful dungeons, good boss and one amazing boss, and the journey from the one dungeon to the other, with the sand sea changing into an actual sea, was just amazing.

If I had to pick 1 section, it would be the sand sea is Skyward Sword.