I didn't find any of these enemies scary, but I'll pick the Redeads considering they were more constant throughout the beginning of OoT like in the grave in Kakariko village and used really well in Castle Town later on.
If i had to pick a scariest enemy over all though (and i will considering i can't find a thread for it) I'd have to say the Great Ocean's Peahats; those giant propeller headed freaky looking joker-style menaces... And my second would be the Wind Waker version of Re-deads, i absolutely LOVED their design and they went a step further with the camera in WW when you came across one, even better because they overshadowed WW Link so much that i did genuinely feel worried for his safety.