Definitely Stone Tower Temple. Many, many things make it harder than Woodfall Temple, Snowhead Temple, and Great Bay Temple.
First of all, there's the whole "the Earth becomes the heavens" principle when you flip the temple. This practically makes it two temples inside one building. In rooms that had a floor before, well they're more difficult because you fall into the sky. Plus, all of the armos turned into Armos Knights, which are hard to defeat if you don't have the Stone Mask (or whatever that one's called).
A second reason it's the hardest is that the Mini-Bosses and Twinmold were brutal. Garo Master alone took me a few faeries to beat. Not to mention I still had the Kokiri Sword at the time :embarrassed: I forget the other mini-bosses name, I think it was Gomess. He was also rather formidable.
The third, final, and most simple reason is that it was the 4th and final dungeon, it was meant to be hard.
Even though Stone Tower Temple was a hard dungeon, it still remains as my favorite Zelda dungeon in the entire series. Not to mention it has awesome music