* Most notably [[DroneOfDread the eerie drones]] that end "Pree-Sisters Swallowing a Donkey's Eye", the {{Squick}}fest that is "Rubby Bulbs", and ''especially'' the climax of "Sailing Through".
* A lot of their lyrics are just... crazy. Like this from "The King of Carrot Flowers Pt. 1":
-->''And your mom would stick a fork right into daddy's shoulder\\
And dad would throw the garbage all across the floor\\
As we would lay and learn what each other's bodies were for''
* '''''IIII LOOOOOVE YOUUUU JEEEEEEEEZUUUUSSSSS CAHHHHRIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIST'''''
* The eerie, low-pitched singing saw drones that open "Two Headed Boy Pt. 2".
* "Sailing Through" ends on a CarefulWithThatAxe moment that actually made one of my friends - a hardened 4chan addict, by the way - ''turn white''. It is utterly harrowing.
* The first guitar strums in "Oh Comely" are innocent enough until you've heard the song through a few times. Then they become the most terrifying sounds imaginable. "I will be with you when you lose your breath," indeed.
* All of [[http://www.youtube.com/watch?v=ReZwDbZQRK8 "Pree Sisters Swallowing a Donkey's Eye."]] Starts out with noisy chaos, then descends slowly into NothingIsScarier as the instruments fade.
** Not to mention that "April 8th", the song that precedes it, has an extremely ominous feel and transitions into "Pree Sisters" without warning.
* [[http://m.youtube.com/watch?v=8p1Swa_pQcY "Invent Yourself A Shortcake"]] is an early set of Neutral Milk Hotel recordings that was self-released in limited quantities during the early '90s. Much of it consists of field recordings and sound experiments done by Jeff Mangum, many of which are quite unsettling.
* "Where You'll Find Me Now" [[LastNoteNightmare ends with a distorted sample of carnival music.]] Kind of cliché, but still creepy if you're hearing it for the first time.
* The ending of "Communist Daughter" is particularly chilling if you happen to be listening to it at night.