The biggest was probably getting the experiment started in the first place. While it can't allow just anyone to annotate anymore, and getting in isn't really that rigorous to begin with. It is still pretty awesome that after a pause from December 10th 2010 to Feburary 24th 2011, a number of the regulars joined together and for over a year have kept annotating and the nakama keeps growing in numbers.
Raiden:"Get to your jets it's time to blow this point" from episode 7 of Mortal Kombat.
The opening for the third season of Captain N got its own video. It features The Unbreakable Annotation winning against Kevin's Zapper.
Midnight Midna calls out The Nutshack for the piece of crap it is in the comments second. Someone notices his handywork and thus insantly gets invited to join despite having zero interest in joining or posting jokes to add.