I actually found the Lanayru scene to be awesome. The fact that Link and Ilia were being represented as the generic Hylian was great, Link getting "killed" by the Interlopers was great, and then that yell he did was also great. The freaky part was probably the many Ilias floating down while Link had that weird "drunken" smile. Bad thoughts came to my mind at that time.
Yep the Lanayru cut scene was definitely the most creepy. Especially when Link kills Ilia and joins among all Dark Links. Also Ilia flying around upside down give me the creeps. The other scene was when Ganon took over Zelda's body. Then Midna laid her hand at Zelda's cheek and she opened her eyes. The creepy yellow color. But also when Link and Midna turned around and possessed Zelda came walking towards them.