Several:
"First she stole my badges, now my lines!" -Red, RGB saga of Pokémon Adventures/Special.
"Even if you select a "No", you're eventually going to have to select the "Yes", so it always ends up the same anyway...that comes up frequently, that sort of thing...but anyways..." - Chimecho, Pokémon Mystery Dungeon: Explorers of Sky, upon selecting "No way!" to Chimecho's offer to let your recruited Pokémon stay at Spinda's Café. (This probably isn't funny; I just spent a hell lot of time laughing at it like the freak I am.)
"Hmph! What are you doing falling down a hole?! Some genius you are! Serves you right!" -Silver, Pokémon Crystal.
"Oh look at what we have here. You're quite the hottie. Why don't you lose that wallflower with you and be my sweetie?"
"Wait a second! Who are you to call me a wallflower? What about me makes me a wallflower?"
"Ahaha! Look at her, she's all serious! Uncool! I'm only teasing out of boredom. A guy like him, he's not to my taste."
"Grrrrr! That's it! I'm furious now! Wes! Be a man; stomp her down!"
"Stomp? Who, me? Ahaha! That's a laugh! Come on then, I'll go easy on you!" - Chaser Emok and Rui, Pokémon Colosseum, in Pyrite Town.
If I remember more, I'll post 'em. Although, one last line, although not particularly humorous:
"Let's kick up a ruckus like there's no tomorrow!" - Lunick/Solana, Pokémon Ranger, in the Go-Rock Base.
