Ted and Lily share a nervous/subconscious tic of peeling off/ripping up labels off bottles (water or beer). Lily does it when she feels guilty (Season 3 Episode 7 Dowisetrepla) while Ted does it when he's nervous (Season 6 Episode 1 Big Days).
The church is the same one Phylis and Bob Vance, Vance Refrigeration got married in on The Office.
Barney's comment "Are you there, Barney? It's me, horny" references Judy Blume's book Are You There God? It's Me, Margaret.
About 11 minutes in, One of Marshall's coworkers yells "spank that butt big fudge" while he is walking down the hall to go home and impregnate Lily. Big Fudge is the nickname Marshall uses at the bar as skee ball champion in Jenkins (season 5 episode 13). It is revealed in season 10 that he earned the nickname through eating a block of fudge to celebrate getting into law school.
Barney's description of Robin having squiggly lines drawn all over her and her appearance refers to Peanuts character Pig-Pen.