Much like your mom and that's what she said, this phrase has a high potential to add innuendo to a previously-uttered statement. Can also be used to augment a comeback.
Person 1: Dude, you suck.
Person 2: No, YOU suck. At night.
Girl 1: So, how are things between you and your boyfriend?
Girl 2: Great! I've never met anyone so awesome!
Asshole 1: At night, that is.
Person 1: I like chillin' with my homeboys. At night.