I just did a did a 100% run of A Link to the Past and I spent 2.5 hour in there. I just couldn't remember were to go and how to get to certain items.
The Great Bay Temple and the Stone Tower Temple from Majora's Mask are both amazing but both need to be completed in a very specific order that is hard for me to remember
The Lakebed Temple in Twilight Princess just turns me around and is massive. It isn't a difficult as any of the previously mentioned dungeons but I find myself looking at the map constantly and I can't run through it quickly like other dungeons.
Last is Jabu Jabu's Belly from Oracle of Ages. It is huge, it has tons of keys and it has multiple levels like the Water Temple in Ocarina of Time. The place were you change the Water levels are also a pain to find and get back to. One mistake and you will be backtracking for a half hout to an hour.