Shaggy and Scooby realize what's happening and take off running
In the episode "Mystery Mask Mix-Up", Shaggy tries pretending to not be scared to keep the masked figure, Zen Tuo, away. How does he do this? He picks up a stick and draws a line on the dirt floor, daring Zen Tuo to cross it. Shaggy does this several times before Zen Tuo finally just takes Shaggy's stick and breaks it.
Also from the same episode, as Shaggy and Scooby escape Zen Tuo, this exchange occurs as they board up a door to hide behind:
Shaggy: Ha! He won't be getting through that door!
[The entire wall the villain's behind lifts up like a curtain.]
Shaggy: ...And wouldn't you know he comes through the wall?
Zen Tuo wasn't done being funny either
Shaggy: Don't you know it's illegal to shoot off fireworks and wreck a store room?
Zen Tuo: We will build a new store room!
Shaggy: I wonder who's gonna build a new us?
In "A Night of Fright Is No Delight", Shaggy takes the fish's fish food for his sandwich, and the snarling sound the fish makes is just hilarious.
Shaggy and Scooby-Doo's barber shop skit in "Who's Afraid of the Big Bad Werewolf?"
Shaggy:[grabs werewolf's paw] Step right in, sir. No waiting. [places him in barbershop chair] I know, just a light trim, sir. We're all wearing it a bit longer these days!
Scooby: Bad nails!
Shaggy:[having given the werewolf a short, uneven haircut] You have a dandruff problem, too, sir! [the werewolf begins growling] Something wrong, sir? Scooby, scat!
From "Never Ape an Ape Man", as Shaggy and Scooby-Doo try on costumes:
Shaggy: Give me liberty, or give me pizza pie.
From the episode "What the Hex Going On?":
Shaggy: Like, I've found a clue.
Fred: Groovy. What is it?
Shaggy: Him. [cut to Shaggy pointing to the ghost of Elias Kingston with his hand on Shaggy's shoulder]
Scooby and Shaggy hiding from Mr. Hyde in a TV set in "Nowhere to Hyde".
Hyde turns on the TV. Shaggy pops up, dressed as a clown.
Shaggy: Hi, folks. Uncle Happy Time here, once again, with your favorite dog star, King of the Wild Blue Yonder.
Scooby[dressed as a pilot, waving]: Hi, kiddies!
Hyde changes the channel. Shaggy and Scooby, dressed as an American Civil War soldier and a Native American, pop up.
Shaggy: If you don't sign the treaty, Running Dog, we'll take back the trinkets and beads!
Scooby: Uh-uh. Indian giver!
Shaggy[sticking his finger into Hyde's stomach]: Then go!
Hyde lifts up the TV
Shaggy[chuckles]: You know, you ought to get this set fixed!