Used awkwardly -- and ONLY awkwardly -- after something you've said to/about the opposite sex (or same, if that's how you go about) could be mistakenly taken into a flirtatious or more-than-friendly context. Replaces "but not like that" in most cases.
"I'm completely positive towards you at the moment, but not in a way that I want to shove my crotch into your face."
Dude 1: Yo, do you like her?
Dude 2: Yeah . . . but not in the mouth.
Dude 1: What the HELL does that MEAN?