In the introductory cutscene, Bianca and the rhynocs sneak in while everyone's asleep and capture the eggs. She accidentally steps on Hunter's tail, causing him to shout and wake everyone up. All the dragons are now eyeing her down, and just when it looks like they might finally do something after all this time... they all just keep staring, and one of them frantically stamps his feet and gestures Hunter to stop her.
Bentley: (After bashing Moneybags several times) One more, perhaps?
Spyro: At least!
In Sunny Villa, one of the resident lions asks you to find his girlfriend, Rapunzel. However, after locating her at the top of a tower, it's revealed that she has a restraining order against him.
Rapunzel: If you see Marco, please tell him I've moved out.
The epilogue you get for getting all the skill points. Special mention to the game of "Whack a Bentley", which shows a mole going after Bentley with his own club, and the seals inventing "squid-boarding".
After you pay off Moneybags to rescue Agent 9, he remarks "You ever seen a bear dance?" He then chases Moneybags around, firing lasers at his feet. It's funnier than it sounds.
Agent 9: Good dancer, isn't he? Not much stamina, though. Too bad, I had a lot more ammo left! *Evil Laugh*
Moneybags referred to Bentley, of all people, as a "dimwitted furball" while he was stuck inside his cage. When he got out, well...
The cutscene leading up to the first boss is rather good. Bianca makes ready to transform a Mook into the first boss, but she botches the spell and instead turns him into a cute little bunny rabbit. The second time she tries, it works, producing a big, scaray-looking toad monster... with a pair of little bunny ears still sprouting from atop its head. After it growls and thrashes around scarily for a few seconds, it abruptly freezes (along with the music) until Bianca magically removes the bunny-ears, at which point it resumes.
Despite being home of the Missing Gem Glitch, it's hilarious how everyone speaks in Haiku, even Moneybags and Sheila.
Even when Moneybags finally stops trying to speak in Haiku, he still somehow speaks in it twice in a row. Spooky Swamp apparently has Haiku magic.
Hunter's mission in Honey Speedway has him in a boat fleeing a flying saucer piloted by a sheep. If you ram your boat one too many times into the various things blocking the boat, the saucer will abduct Hunter. Hunter's reaction when he gets lifted in the air by the tractor beam? A broad smile and gently waggling his arms around.
In one of Icy Peak's sublevels, you have to protect you-sized Nancy the ice skater from some giant bullying hockey players. If you fail to flame one in time, they use her as a puck, sending her flying with a loud slap and leaving her knocked out face down on the ice. She then claims it didn't hurt as much as it looked.