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The Annotated Series
In Captain N 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.
When the annotators respond to the smurfing in Captain N S3E2 by going out of their way to add to the Hurricane of Puns.
Season 1, Episode 11 of Captain N 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 of Captain N 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. It got more hilarious after the annotators defended it when Lana said it wasn't funny.
Bubsy's shirt was alarmed by Solid Snake.
"Cthulhu was definitely a top tier Street Fighter II character."
From Food Fight.
Mr Clipboard: Your cuh-cuh-cuh *smacks self in head to finish 'customers'.*
From the same film a single annotation perfectly sums up much of the film.
Revealed villain: All I ever wanted was you (Dax)!
Annotation: All I ever wanted was to have sex with a dog!
Least I Could Do...
Rayne: It's a real event! It has ribbons...okay I know the color is kind of ugly *holds up yellow support ribbon* Most of the good ones were taken.
Annotation: The yellow ribbon actually represents, among other things, suicide prevention awareness, which I'm afraid is something I cannot support in this context.
In Sonic Underground, Robotnik's plan in Episode 35 is summed up as thus and the reaction to it:
So let me see if I got this
Step 1. DROWN THE ENTIRE PLANET
Step 2. Watch Sonic be all butthurt.
Robotnik: Master Troll
In Pryde Of The X-Men Magneto spends much of the pilot abusing Lockheed. When this predictably causes Lockheed to betray and attack him one of the animators gives Magneto a word balloon that declares " I'VE BEEN NOTHING BUT NICE TO YOU!"
SMB3 the Annotated Series
Larry/Cheatsy calls himself the "Emperor of Eavesdropping" in one episode, leading to many hilarious "I am the [Title] of [Alliterative action]" jokes.