I know it's not a 'children's' show, but The Regular Show is so weird and disturbing.
Yo Gabba Gabba (the worst it makes me puke)
The Jungle Book: Water Rescue
All the kid shows that are the worst shows in United States History
Candle Cove - it was on in the 70's, it was kind of a scary puppet show that involved a smiling ship called Laughingstock, a dumb pirate, a little girl and a villain called Skin-Taker.
I swear Boobas was a creepy show.