The Lavender Town Tone thing is definitely the oldest thing that creeped people out about Pokemon. Honestly it did give me headaches and made me depressed whenever I got to Lavender. Maybe its just because its really annoying.
Most of my favorites are the ones that can be believable.
I don't know if I've come across a really believable one to be honest. Granted I've only read like five.
I should write a creepy pasta one day!