Hubie and Rocko being scared by a thunderstorm. What Rocko says as he and Hubie run around trying to avoid being struck by lightning sells it.
Rocko: Fire in the sky! Fire in the sky, fire in the sky! Hide, hide, hide, hide!
Rocko's reaction after Hubie told him that Waldo (a penguin Hubie mentioned early in the film) is not real
Rocko's line when they're faced with Killer Whales, and Hubie loses his pebble again.
Rocko: Pebble? Your pebble? Forget about the blasted pebble! I don't wanna hear "pebble" from you!
The entire "Good Ship Misery" song is so over-the-top (and a bit disgusting) that it's really funny.
The funniest scene is the scene where the penguins turn into bowling balls and hit the other penguins.
Just after he swam into the leopard seal's mouth to save Hubie, Rocko whooped loudly inside, causing the leopard seal to shake while unintentionally opening its mouth to let the penguins swim free. The expression on its face as it happened was priceless, too.