Through out the anime, movie and manga, there are some parts of Naruto scenes that is very funny. Which part of them are funny and why
I'll start it with 2 scenes
scene: Anime - where Maito Gai and Rock Lee have to fight each other in order to escape from the trap inside the building :: there is a scene where both of them send Morse Code by tapping their feet on the floor
why: They both are very expressive persons right on their behaviour as well as their responses. It is very funny when they both are crying while reading the Morse Code
scene: Manga - where Tobi, a new guy join Akatsuki and started a "small fight" with Deidara ( Sorry if I mispell the name )
why: Tobi is quite straightforward man where his word sometimes or we say most of the time intimidate Deidara
How about u guys?
I like the part when Naruto farted at Kiba at defeated him by that 
Scene - Hinata sees Naruto after his 2 1/2 year of training with Jiraiya and hides behind the corner, all frozen.
Why - After 2 1/2 years, Hinata is still attracted to the little freak and still has the same responses as in Naruto Part 1.
Scene - Kakashi, Naruto, and Yamato explains to Naruto that the Rasengan is an incomplete jutsu and it was intended to have the Wind element imbued into it. Naruto learns that he can overcome this by making a third clone.
Why - 2 Jounins couldn't figure out such a simple thing for Naruto to add Wind element into his Rasengan, and Naruto was the one who figured it out. C'mon, Naruto, after 2 1/2 years, he added a new Harem no Jutsu and some other techniques into his collection, but that still means he's pretty dumb. Did I mention that 2 Jounins got outsmarted by Naruto?
lol, any scene of Naruto participe is funny XDD,
Un saludo,
Matta ne~
Hahahaha .. agree
but, sometimes, he has very touching scene as well when he really wants to sacrifice himself for someone or when the topic has something to do with monster
Scene: When Naruto kiss Sasuke accidentaly.
Why: I think is funny when Sakura and all the other girls beat Naruto for Kissing Sasuke.
really cracks me up whenever he does that techniques he made which transforms him into a naked girl!! 
another really funny scene is when he asked that hokage's grandson, forgot his name, to transform into a hot babe but came out as a fat, seriously ugly babe with thick lips... 
Scene: Naruto sees Hinata training naked in front of a waterfall.
Why: As it was dark, Naruto didn't recognize Hinata, but as he was telling Kiba what he saw, he claimed that it was an "extremely attractive girl". Of course, Hinata was just two steps away from Naruto, and she turns deep red when she hears this. Again, Naruto has known Hinata for quite a few years and never noticed it? He had to see her naked profile in the waterfall to realize it? And how unfortunate is Hinata, as the only time Naruto really did "notice her", he didn't recognize her...
Id have to say...
Scene: Anime - Naruto and others are stuck in the genjutsi place, which that girl (i forget her name, the one who's powers were taken by kurenai) casted, so that konoha looked like it was in ruins. I thought narutos method of getting through the fire in the corridor was good XD. He summons a load of cl,ones to beat him up and chuck him through the fire so he doesnt feel it
.
Why - Its just typical naruto, and the concept of watching his get beaten up by himself is quite good. I always like the EYES that they give him when he's shocked
.
Scene: Anime - Naruto is evading some enemies in the woods (the menma arc). A load of kunai's are thrown at him, and he hides behind a tree and he thinks he's safe when they hit the tree. Then he looks round and see's that theyre attatched to exploding notes
. There goes the eyes again
.
Why - His reaction is just great
Scene: Anime - When naruto and the boss frog are fighting the water giant thing (kaima arc). The boss from tells him to use a fire technique to spark off his oil, and naruto goes beserk
Why: Naruto doesnt know a fire technique, and suddenly panics XD
Almost every scene involving Naruto is funny, but I mean mostly for season one.
Scene: I liked the part where Naruto plead Jiraya to train him by using "Sexy no Jutsu".
Why: Of course, I don't need to say anymore. Two pervets together. 
i like naruto expression when he found out Jiraya spent all his pocket money in drinking and woman. haha damn funny
CMA - that part when Naruto saw Hinata at the waterfall was hilarious. Poor Hinata... she must have been soo embarassed!
Scene - Beginning of the Bikouchuu arc. Naruto was in the hospital visiting someone and Hinata comes in the door. Naruto pops up upsidedown in front of her and confronts Tsunade about going to find Sasuke. He finally realizes Hinata is in front of him and she turns all red. He asks her if she has a fever and touches her forehead. Hinata gets startled and hits her head against him and Naruto flies back and 'flops' back down. xD
Why - I just thought when Naruto flops. xD
Scene - All of episode 103 when Sasuke, Sakura and Naruto try to spy on Kakashi and find out what he looks like under his mask.
Why - This is probably the funniest episode I've ever seen. I love how they imagine Kakashi to have buck-teeth and big lips.
Scene - I think it was episode 124 with Lee fighting that bone guy. Lee accidently drank some sake and he turned into a drunken fist master.
Why - Watching Lee getting drunk and fighting is hilarious! I love how he's so random with all of his moves. And the part when he pretends to be asleep is hilarious!