None of the episodes are really scary, because they always have the humor aspect. But the episodes that have the "scary" theme are some of my favorites. Like The Graveyard Shift, Nasty Patty, Night Light, and Scaredy Pants. They all have that theme, and it's set mostly during night time, which I love.
So, to answer your question:
The Graveyard Shift
Nasty Patty
Scaredy Pants
Night Light
Once Bitten
Toy Store of Doom
Hall Monitor(Because of the last couple minutes)
Shanghaied
Ghost Host
Fear of a Krabby Patty(If you're afraid of Killer Krabby Patties)