The third movie, when Chucky's on the computer in a dimly lit office. His reflection is really ugly at that moment, even for Chucky!
Chucky's death sequence in the second movie. He deserved it, but DAMN.
The first appearance of Glen's Glenda persona. If Chucky is freaked out by her, you know something is wrong.
When Andy is locked up in the asylum. This kid is able to relax for a bit as despite where he is, he's at least away from Chucky. But then he sees Chucky coming for him out from his window. He tries to get the Doctor's attention, but the doctor doesn't believe him. So all he could do for now is huddle in a corner and cry knowing how screwed he is. Until he faked Chucky out and got away.
Several of the death scenes in the series can make watchers feel uneasy. The aforementioned Doctor's death, being eletrocuted until blood comes out of his eyesockets, the businessman being suffocated in his car on the second film, the garbage man being crushed in his own truck, Joan being burned alive....
In the first film, Andy's mom found Charles' old apartment room: with the walls decorated with painting depicting a voodoo ritual, a creepy sculpture of people melded together, and writing on the wall ("Oh thank you, mighty Damballa for life after death") written in blood.
In Seed Of Chucky, when the special effects guy unscrews the back of the Tiffany Doll...only to find a bloody spine!