The ninja Meowth remarking to Team Rocket's Meowth, ""They're taking the gym challenge, I know where they're going. You don't think we have to run an obstacle course every time we need a pint of milk, do you?"
Bulbsaur overdoing the Growth job and accidentally evolving into a Ivysaur.
Ash remarking ""Not only no, but HELL no" about Maiden's Peak.
Palkia, the Titan of Space, smiting Sir Aaron's character sheet because of a bad break-up with Kyogre.
Not only does the character sheet get smited, but it gets compressed into neutronium.
The Indigo League commentator remarks after Ivysaur takes down a Jaxon's Muk: "Okay, ladies and gentlemen, after a talk with our local Joy, I can tell you that Jaxon's Muk is not permanently harmed. If you have a piece of sludge near you, those in the front rows, please signal and a bag will be provided. Muk is going to be reincorporated later, and will be fine so long as not too much mass is missing."
Ash and the company talking about the Australian Dragonite King.
Ritchie: Yeah! Actually, now I think about it I do recognize you. You're that trainer they were calling the Gym Destroyer on the TV commentary, right?
Ash: I didn't know they were calling me that. Though I have to admit it's pretty accurate...
Ash stating that, using Aura Purge, he'll get rid of Misty's fear of Bug types. Riolu says that Misty'd kill him if he suggested she's weak. Ash says he'll use "Tact and Diplomacy". Riolu simply sighs and replies with "You're Doomed."
Followed up by Ash threatening Misty that either she takes the painless Aura Purge to get rid of her fear of Bugs, or Squirtle "Fixes" her with sheer distilled awesome, possibly involving tearing open dimensions, rock music from nowhere and punches.
Even funnier? Squirtle still manages to at least partially fix her using Gurren Lagann logic.
Dexter, Dee and Damos have their own little nickname: The Three Pings.
Pikachu and Riolu. If they're not arguing, they're snarking about something.
The one second long "Fight", if you could call it that, between Pikachu and Surge's Raichu.
This exchange between Jessie and Butch.
Jessie: "Well, well, wouldn't have expected to meet you here, bit-"
About the gym battle... It started with Lapras using Rain Dance... Indoor. No effect on the field, but it was making rain on the vacation resort outside. Then we had Ash's strategy for the match (a double battle in which he used Lapras and ''Snorlax), whose result was "a half-ton Pokemon bouncing around on an icy surface like a crazed hockey puck, periodically shooting intense Hyper Beams". It's funny... And devastating.
Mewtwo's acceptance of pretty much being a plot device whose function is to limit the collateral damage done by Ash. Sabrina's reaction makes it all the better.
We finally got an hint of what happened between Brock and Professor Ivy. Thankfully, Brock had forewarning thanks to the time travel, so it got well.