In the last scene, the swords from Ted and Marshall's duel and the mother's yellow umbrella are visible on the wall of Ted's home.
At one point Robin's brain says, "That's it. I am outta here." accompanied by footsteps and a slaming door. Homer Simpson's brain does the exact same thing in an episode of The Simpsons.
When Barney spills ketchup on his tie, you can briefly see his shirt under the tie is also stained.