Hmm, imo I would say the creepiest character in LoZ would have to be the working boss man character in oot, he is always laughing, even when things aren't funny...
The Zelda franchise is packed full of creepy characters; many are creepier than the one I’m about to choose but this guy has always stood out to me and never ceases to give me an uncomfortable chill when I encounter him. The Happy Mask Salesman.