My favorite place in Majora's Mask was absolutely the Ikana area, i had a hard time figuring out what do do there. In the first place i must go to the Gorman track for the Garo's Mask. Then the Graveyard of Ikana for the Song of storms and beat Sharp down with it. I like Dark places in overall, Ikana was a great example of one of the darkest places all over the Zelda series. I love the broken Castle of Ikana and the King Igos. They were all doomed by the darkness of the Stone Tower, after you beat Igos he said ''Shine the Light of Justice'' The place had great folks but it stay a dark place for me. I really enjoyed the Stone Tower Temple, the sound track was great and i like the Upside Down system.
As for in OoT i enjoyed the Ganon's Castle. All the little riddles for breaking the Barrier were fun to do and you see all the parts of the Temple's back again. I like the Fire Temple and Shadow Temple too, but the Ganon's Castle was epic. The Tower Section to Ganondorf was also a great challenge.
I was happy in the past to beat the game till Ganon's Castle, i got stuck for a real long time in the Water Temple.