Any of “the Little Rascals” shorts that starred a young Robert Blake.
“the Brood” (lotsa creepy faceless boogersnots)
“Village of the Damned” (This is the movie that was satirized in “the Simpsons” episode when all Springfield kids were put under curfew by Chief Wiggums.)
Does “Napoleon Dynamite” count? But that kid who dances lamely in the commercials sure looked goony enough…
The kid in the Indian in the Cupboard movie gave me the creeps, for some reason. It’s been awhile, so I can’t remember if it was his personality, his voice, his face, or his name that got to me the most…it might have been one factor that pushed him over the “creepy” boundry, or perhaps it was just creepy synergy from the stew of creepy that he was made out of.
Buddy, aka Incredi-Boy, aka Syndrome from THE INCREDIBLES.
Rose Red and *Firestarter *
Steven King seems to have many movies with a creepy, weird little kid.
*The Other *
Good horror story about twin brothers.
Phone, which isn’t a great movie, does have an ultra-creepy little girl who becomes possessed. The girl was far better than the rest of the film.
I just watched A Tale of Two Sisters, and as you might guess, there are two creepy little girls to enjoy in that one.
Good call on The Tin Drum. I saw that movie when I was far too young to really know what was going on, and Oskar kind of messed me up.
Escape to Witch Mountain
and anything staring Margaret O’Brien, especially The Secret Garden.
Willy/Milly, aka Something Special: the main character is a teenager, but there is a creepy young boy (who may or may not be God) who figures heavily into the plot played by a **very ** young Seth Green.
I don’t have any new ones to add, but I had to say something when I saw that there was another “Manitou” fan out there! I thought I was the only one. 
“Guard well the pips, and the fruit shall grow without let!”
The Red Balloon and Hand in Hand–both shown during assembly at my Catholic grammar school. The latter was a story about the friendship between a Catholic boy and a Jewish girl. The kids weren’t that creepy, but after the little girl fell into the river–I swear I had drowning nightmares for weeks!
“The Bloodening”
“But your the ones who’ve been bad. We know that you and the bootblack were rogering the fishwife in the crumpetshop!”
Amen!
Dennis the Menace
Anything involving cheerleaders, Mary-Kate & Ashley or Dakota Fanning (ie. Cat in the Hat shiver)
How was he creepy?
I wouldn’t count Harriet, or Dawn from Welcome to the Dollhouse as creepy either. Harriet was a smartass, not disturbing, and poor Dawn doesn’t mean any harm!