- The Hexagon Brothers, though they're more like mooks. To be fair, it's just their outfits that make them funny. They're actually pretty strong in a fight.
Greesix: Seven!Resix: Eight-Wait, what?! How can there be more of us?
- All of their scenes with them failing to count off properly are still pretty funny, though.
(looks around at his five brothers)Resix: Brothers, beware! There may be spies among us!
- Chobin; sometimes he's worse than Miror B.
- Michael's sister Jovi playing with one of the lab employees. At first she forgets they were playing hide and seek and he falls asleep while hiding... and at some point Jovi found him and doodled on his face.
- Later he says that he played house with her. Jovi was the dad and he was the mom. He then asks Michael if he would like to join next time as the baby.
- Then he says he played Mock Pokémon Battles with her. Jovi was the trainer and he was the Poké Ball.
- Setting aside her Moral Event Horizon, Lovrina and her "So" Verbal Tic can be pretty hilarious.
- Snattle's running animation.
- When arranging the Pokemon in the purification chamber, their idle animations seem to synchronyze just too well to the background music, making it seem like they are dancing.
- An easily-missed moment: After visiting the Poké Spots for the first time but before the attack on Phenac, go to Agate and talk to Eagun. He will bring up the wild Pokémon, then mention that it might be "nice" to raise one of his own. Pikachu will then give an offended shriek.
- Senilor claiming that he saw a flying Wailord. Which his son dismisses as him going senile. If you know your Pokédex entries, you would know that Wailord is classed as the Float Whale Pokémon; with its height and weight, it is less dense then air essentially Which very likely implies Senilor really did see a flying Wailord.
- Later on, when you find the S.S. Libra ship, you return to tell him that what he saw was in fact a ship being lifted through the sky. Senilor dismises that as nonsense.
- At one point, Michael gets attacked by members of Team Snagem who use Sleep Powder on him and steal his Snag Machine, so that means you have to go to their hideout and get it back. When you find it, you see that the extremely muscular Gonzap is unable to wear the Snag Machine designed to be worn by a child, which he even outright points out to his underlings.
- Even funnier when you consider what this means about Wes' Snag Machine from Colosseum, which had a sizeable pauldron that gave him half-Shoulders of Doom and a wire coiled around his arm. Wes took a Snag Machine (possibly) meant to be used by someone much larger than him and managed to work with it just fine, but it obviously doesn't work the other way around.
Funny / Pokémon XD: Gale of Darkness