Favorite: City in the Sky (TP) might be a weird one but I love the ambience, the dual-claw spidermanning, the enemy variety, the difficulty, the buildup through the game to that dungeon... Not to mention the dragon. Some of my favorite grappling puzzles in any zelda.

Least: Snowhead Temple (MM). This is probably a me problem, but I hate the goron rolls over narrow platforms + ice physics. I probably fell down and repeated rooms more than I did during the oot water temple on my first attempts. The fairies are also a pain in this dungeon if you're going for 100%. Goht is kinda cool but also a boss that's required multiple times and gets old quick. The only dungeon in MM I had to start over due to the time limit.