I have a tie between two: Pic related and N's childhood room, specifically the one in B2W2.
Lusamine was already fucked up. Coming into a room where she has Pokemon literally frozen, for her own display of beauty, was dark as fuck for a game catered for kids.
The king of creepiness has to go to N's room, though. It was a neat easter egg within the first game, but holy shit, in the sequels, it stands so well with Team Plasma as a whole.
Not to mention the theme is Lavender Town 2.
https://www.youtube.com/watch?v=nmZ5pSjeQVc