Honestly, I found the Snowpeak Ruins perhaps one of the most difficult dungeons in the game, if not the most difficult in my opinion. I think the major reason is because a lot of precise movement is required to stay alive in quite a few of the rooms, mainly with the ice near the bottomless pits.
The room I found the most annoying for me, in that game, was the one where you had to navigate across the rafters, the floor nonexistent. I like ice puzzles, especially with blocks, but when it comes to navigating ice by foot, I'm baffled.
The only other dungeon I found difficult was the Lakebed Temple, but I found it difficult only when you do not complete the game in one sitting. If I go through it in one sitting, I can breeze through it; however, if I save and quit, I easily lose track of where I've been, all thanks to the central room of the temple.