I have never had the guts to go back the the Great Deku Tree after his death.
I actually had my younger brothers go in there for me to get the Skulltulas you couldn't get in the first run though it.
Also, Half-Life 2, while not really scary in that kind of way, every once in a while one of the headcrab cunts will jump at me from close range in a dark place, causing me to flinch and accidentally press Mouse 2 and launch an SMG grenade at it. At point blank.
And don't get me started on the headcrabs in the vents in the first game. Goddamn little bastards.