Just... O.K.? is something Barney says when he is either caught lying or nobody wants to do the same thing he wants.
Barney caught lying about the Dutch ambassador when told that the ambassador was a woman - Robots Versus Wrestlers.
Barney insisting on Ted wearing a brobe during The Broath - The Broath.
John Clifford Larrabee, who looks like Barney, appeared in Ted's dream and tries to convince Ted that it's a dream - Landmarks.
Barney guiding Ted with one of his Playbook plays when Ted complains about the play being ridiculous (Barney says: "...just... ok, over? Ok, over?" because he was talking through the radio". - Weekend at Barney's.
Barney insisting that Ted be the one working with the Nazis in his re-enactment of Indiana Jones and the Holy Grail. - Knight Vision.
When Barney has the yips and Heidi Klum gives him advice and he leans in to kiss her. She walks away, then he claims to have made out with her. - The Yips
Ted uses the phrase in Ducky Tie