The Sycopated Clock. It was the theme to the Late, Late Movie when I was about 7. The song still gives me the willies.
When I was about 8 or 9 years old, I was spending the night with a friend who lived across the street. After we went to bed, her dad stayed up and was drinking. He had this record and played this song over and over. I thought I was going to go insane. Finally, after about the 10th time (no joke!), I got up, and went home. So, yes, this song always creeps me out.
My other pick is “You Might Think” by The Cars. I think I was about 12 years old, and I listened to my alarm clock/sleep timer before going to bed. I remember this song coming on and the part where the music stops and it goes, “But you kept it going, till the sun went down. <Bump> You kept it…going.” I turned my radio off because it creeped me out so much.
“Got my mind set on you” by George Harrison. That video would scare any 6 year old. =)
That song by that partdrige kid “I think I love you”
It jsut starts out so slow and is such a dark tune… Oh well I got a weird Childhood
Ahhh… Napoleon XIV Truly a classic.
For me it was “Sheep” by Pink Floyd, from the “Animals” CD.
When I was a kid my mom used to watch those horrible religious shows, and one of them had a rock expose’ about things like Floyd, “Hotel California,” “Stairway to Heaven,” etc. For the longest time the synthesized voice doing its own version of the Lord’s Prayer creeped me out.
The song still creeps me a bit, but now I like it.
Harry Chapin’s “Cats in the Cradle” was so morbidly morose that I couldn’t stand to listen to it. AC/DC and “Highway to Hell” seemed a lightweight parody
Heh. I read this thread title and immediately I started hearing, “We had joy, we had fun, we had seasons in the sun…” in that whiny nasal tenor voice…
It’s just so… morbid. “Goodbye, my friend, it’s hard to die…” And although in 1974 I wasn’t exactly a kid, still I was a “old teen”, and I still was completely creeped out every time I heard it on the radio.
http://www.clinton.net/~sammy/seasons.htm
This website is going to play a Casio instrumental version for you and you can sing along with the lyrics. No bouncing ball, though. 
Girl Land and Boy Land by Marlo Thomas wigged me all the hell out as a kid. I had many reoccuring nightmares over this freaky-ass song.
Imagine a evil clown singing over merry-go-round music. That’s how I remember this song.
See you in Hell, Ms Thomas.
Everyone who knows The Syncopated Clock says I’m crazy for thinking that it’s creepy. They all say it’s a fun song. Ha! I say from under my covers. There’s a sample of it here: http://www.molenaar.com/general/article/mp3/03214405.mp3 Is this song not scary?
Oh, and how could I forget the song that terrorized me during my pre-school years,
*The worms go in, the worms go out
through your stomach and out your mouth. . .
Comfortably Numb by Pink Floyd. My older sister’s room shared a thin hardboard wall with mine, and one of her speakers was right against this wall near the headboard of my bed. I’d just be trying to sleep and I’d hear this voice saying Hello? [echo] Is there anybody in there? and it would scare me muchly.
I wasn’t young when I first heard it, but I will NOT listen to Pink Floyd’s Dark Side of the Moon album alone.
“Maxwell’s Silver Hammer” by the Beatles creeped me out when I was younger.
Vincent by Don McLean. Creepy and depressing. It wasn’t until sophomore year in college that I finally figured out the song was about Vincent van Gogh, not a tribute by DMcL to a family member. Still creepy.
Revolution #9 by the Beatles. Just because it’s so wierd. Backwards music still gives me the creeps for some reason.
Creepiest song I remember…
And When I Die by Blood Sweat and Tears
We had it on an old Dolby Hits Collection tape.
At the beginning of the song? That’s not the way I remember it. I seem to remember about 20 minutes of soothing noodling to lull you into a false sense of security and put you into a sort of twilight zone between waking and sleep, and then the ultraviolence.
First time I heard it, I was about 14, and I had to change my shorts.
You said it, sister. Wanna hear even creepier? When I was a kid, our church choir director had us sing the words to Amazing Grace to that tune.
Talk about weird…
Sounds cool, though.
I downloaded a few of these last night, especially the ones I remember, such as “Dark Lady,” “The Night the Lights…,” and “Angie Baby.”
It’s really funny that these were so scary, because they’re mostly silly. “Dark Lady,” which gave me the heebiest of jeebies as a kid is just GOOFY!
Dies Irae 
“Good Night” from the Beatles’ “White Album”. So overly nice that it’s creepy. Almost “Sleep so well you’ll never wake up.”
From “Abbey Road”:
“Come Together”
“I Want You (She’s So Heavy)” - the way it just abruptly stops is weird.
Wild Fire and The Wreck of the Edmund Fitzgerald.
I didn’t run screaming from the room but if heard them at night I would let my imagination run wild. (I kind of enjoy being scared so it was kind of fun)