In "Claydol Big and Tall"
The entire maiden scene. Claydol making Jessie, May, and Meowth blast off before chasing after Wobuffett with hearts in its eyes. Then Ash sending Swellow in to save it and it only getting its wig. Then the proceeding look on Swellow's face.
There are lots more funny moments, this is just the one most clear in my head. Jeff Zero had a bunch of good ones.
Jesse: Listen to me kid, when you get involved with the oppisite sex your only asking for trouble
James: Yes, and thats the kind of trouble I stay out of.
Meowth: Yous two don't need the oppisite sex cause' yous got each other
Jesse: Whats that supposed to mean?
James: Not Funny
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Melody: Well, I hope your happy, Mr. Hero. If you'd just listened to me in the first place and stayed at the party like I told you to, we wouldn't be stranded out here on this island.
Misty: Welcome to my world. I have to deal with his stubborn attitude every single day.
Melody: Oh, you'll get used to it. It's just something you're gonna need to work on when the two of you get married.
Misty: Take that back!
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Melody: What are you coming for?
Misty: To find Ash. And before you start saying it's because I secretly like him, don't. Because I don't.
Melody: Hey, chill out. You sure are sensitive about someone whose not your boyfriend.
Misty: He's not my boyfriend! He's a boy and he's a friend, but he's not a boyfriend!
My favorite funny part was when Pachirisu keeps running and the other Pokemon were chasing it.
Some Of Meowths Day-dreams Lol
In All things Bright and Beautifly when Jessie tells Seviper to use Sacred Fire
James dancing around in a Moltres costume somewhere in Johto
In Having a Wailord of a Time when Ash and Max try to look after the starter Pokemon
Abandon Ship when they're all hanging around on the ropes greeting and fighting each other XD
Ash: I'm an apple for a day but I need a doctor right away
Ash: Muscle over mind!
Not my favourite but there are so many funny moments through 500 episodes that there's no way you can remember them all