In the Season 11 finale, Sam is forced into reading signs. He says he needs a "chronological caption with a lame font". Cut to a caption in Comic Sans with a silly noise.
The Christmas specials, of which there have been four so far, feature the resident Butt-Monkey Radar Overseer Scotty receiving burnt cookies for Christmas. On the fourth time, Scotty completely spazzes out after he spent the beginning of the video repeatedly stating how sick he is of this Running Gag.
In Season 14 Episode 6, the scene where Scotty and Bacon are talking over each other, arguing about baloney and bacon.