Ibuki's storyline from 3rd Strike had her politely challenging Oro to fight as her final exam of her ninja training. Ultracentenarian Oro didn't take the request too well, since he expected that the young girl approaching him was going to ask him out on a date.
Sean's ending in 3rd Strike. It stars with him raising his arms in victory, then fades to him on his back after his opponent beat the everloving shit out of him in the first round of the tournament while Ken tried to wake him up, meaning his ending was All Just a Dream. Oh, and his opponent in the first round was Ken. It was a curb stomp battle.
Knocking out Twelve with any kind of attack that makes your opponent collapse (usually a LP or LK). He croaks out a "Give...up..." before his body deflates and loses all definition, leaving what looks like a skeleton wrapped in plastic in a heap on the ground.
One of Twelve's victory animations is also pretty funny. He looks around to make sure nobody is looking at him, before jumping up in the air and turning his arms into wings and flying away, and letting out a "Woo-hoo!"
The infamous groin attack in Ken's New Generation/2nd Impact ending courtesy of his 5 year old son. What makes it so hilarious is how the whole scene is shown and paced. Ken is first seen telling someone named "Mel" to attack, but we can't see this "Mel" and it's also the first time that someone named "Mel" is mentioned in the Street Fighter canon. Then the scene changes and we see Ken look as if he had been fatally injured, followed by Eliza's horrified screams. Only then do we see who "Mel" is: the tiny little kid who barely reaches Ken's knees had punched his dad in the nuts.The punchline in itself is worth several lulz.
Gill's 3rd Strike ending has a minor one. As he's giving a speech to the people he's going to lead to "paradise", you can see many of the other fighters, who listen in awe, or at least seem quite interested. Except for Akuma, that is, who crosses his arms and looks away in boredom, as if to say "Tsk, what a load of bullshit...".