In S2E11, Wombatman tells Kid Icarus to "take a speech class to get rid of that -icus problem." Cue wall of annotations proclaiming Wombatman as great as Simon. Doubles as a Crowning Moment of Awesome.
Season 1, Episode 11 has a lot of the questions about the mirror world, but this is probably one of the most amusing:
So in the mirror world has the chicken or the egg debate looped around forever too or has it been solved?
Season 3, Episode 7 had the Prince pass out via magic potion, and had his face land right into his bowl of soup. The annotations noted that this was the only thing humorous in the third season. Than when Lana says it wasn't funny, the Annotators get mad and defend it.
Ethan's Everquest character sets Lucas's on fire three times. The first two times Lucas just stands there silently. The third time he actually screams, causing someone to comment "Third time's the charm apparently".