I wanna say it goes back to golden age Hollywood movies where they want to hint to the audience that a character has a sinister motive or agenda that isn't immediately known to the other characters in the scene.

Recent uses of it make it a lot more obvious that the character that says it is up to no good. As you mentioned, South Park had used it quite a bit. I remember it coming up in Community too. I don't remember which episode, but I wanna say Britta uses it in a meta way that the other characters immediately recognize she's planning to sabotage the situation.

This is the first time me moderating c/southpark has been relevant.

Can you provide a video example? Any example doesn't have to be this one.