Crowning Moment of Funny: This scene in the black and white flashback Kakashi has in Episode 23:
Kurenai: (In black and white flashback) Kakashi, protect me... With your penis! Asuma: Me too. (Snaps back to present/colored Asuma for a second, to Kakashi) The hell, man!?!
His southern accent makes it sound hilarious.
Sorry, but quite frankly this one's funnier:
Kurenai:(same black and white deal) "Kakashi, save me, you sexy, sexy man!" Asuma: "Yeah, save us... You sexy, sexy man." (Reverts to present) "Okay, I did NAWT say that!"
What makes it even better is how Asuma objects throughout the flashback, while Kurenai calmly waits for him to finish before calling him out on his bullshit.
Then afterwards we get Kurenai's response to the flashback.
Kurenai: Honestly, what would Anko say if she heard you talking about me like that?
Anko:(off screen) Whooo! Threesome!
"Japanese Hitler!!!"
Sasuke has learned the ability to defeat his brother and the log... (Beat) ...Yeah, no.
"Everyone... loves.. the carameldansen...."
The running theme of the horror that is Gai's naked body.
"Really? The villains of this arc are the Map Quest ninjas?"
"Hold on Vegeta! In a later arc, they bring back Mizuki."
"God damnit I hate filler arcs.."
"I'm Gaara. Of the Funk."
* LOG'D!*
Zabuza's unmasked voice: Jerry Lewis. "What? Oh no, the lady! The pretty lady with the way of the dying! Why'd she have to die?" "Why are you attacking me when I'm grieving over the pretty lady! She was so pretty and lady! Good-bye to the mousie!" "Oh, nice Kakashi person, can you revive me and the pretty lady with the Dragonballs?"
"Are you done? You sure? 'Cause I'm not going to get interrupted again by that stupid plot! Okay then. Haku, you're min—* scene cut* SON OF A FUC(bleep) MIS(bleep) CUN(bleep bleeeep) BALONEY!"
When Kurenai and Asuma confront Itachi and Kisame, Itachi asks them whether it was their Akatsuki robes or their evil chakra that clued them in. Asuma says that it was the evil chakra, only for Kurenai to reveal that Asuma actually noticed that they didn't leave a tip.
Kakashi's flashback of his fight with Itachi and Kisame involves him being overly heroic, Itachi and Kisame as Evil Brits complete with mustaches and monocles, and Kurenai (and Asuma) treating him like a sex god.
Kurenai:(flashback) Kakashi! Protect me...with your penis.
Asuma:(flashback) Me too!
Asuma:(reality) The hell man!
Naruto singing "Living in the Sunlight, Loving in the Moonlight".
Kakashi and Jiraya's conversation in episode 28, after Sasuke and Naruto's fight:
Jiraya: Shouldn't you be keeping an eye on [Sasuke]? You know, the only one you actually have left?
Kakashi: I guess you're right.. At this rate, he and Naruto will become like you and Orochimaru were!
"You have to get out of the village!" She said. "The cherry blossoms are coming, and they're going to take away my tortillas! Get that cow out of the way!" *moo*
Hee hee, *moo*.
Naruto summoning Gamabunta to fight Gaara. Objectively the funniest moment in the series.
