Everything about Fred's ridiculously complex trap, from the fact that he does absolutely nothing while it's happening to the spectacular failure it produces. In fact, most of the self-parody in the show is brilliantly handled.
This exchange with the villain.
Daphne: But you already have a job as a teacher, why would you need more money? Raffalow: *stares back at them* Everyone: Oh right... haha... my bad.
One thing I love is Velma's deadpan, unenthusiastic droning while she work as the "Ghoulish Guide" for the Crystal Cove Haunted Tour while everyone there reacts to what she says with intrigue and horror about the legends. She clearly hates her job and snarks at every opportunity, even once pulling out a tape recorder that makes a screaming sound with the most unenthusiastic expression possible while everyone else reacts with horror. One particularly great scene is:
Velma: The first documented case of the Curse of Crystal Cove is from 1630, when a garrison of Spanish conquistadors mysteriously vanished from the harbor.
Customer: Oh that is so scary! Where did they go?
Velma: What part of the word mystery didn't you understand?
When Daphne's parents ask her what she sees in Fredd:
Daphne: He's like one of those geniuses who aren't appreciated until they're dead.
Freddie goes over to talk to the Sheriff about the mystery. The Sheriff's not in a talkative mood. Freddie decides to steal one of the corpses and starts screaming at the gang to start the van, as he runs over, corpse tucked under his arm, the most hilarious expressions on everybody's faces.
Daphne: It's not your fault Fred. We all helped steal the body.
Everything about Fred stealing the body, from him running away with it right after Daphne said he'd talk to the Sheriff about it, to Fred and Shaggy bringing it into a classroom and causing everybody to run away screaming.
Velma's first snarky line.
Sheriff Stone: Just cork it. You see this badge? You know why it's here?
Velma: It came with the shirt?
Episode 2: The Creeping Creatures
The increasingly ridiculous but apparently completely true montage about Gatorburg's "gator mining" economy. Ending a gator oil well, spewing out hundreds of alligators into the sky like oil.
Greta: I got a few hotel rules. Rule #1: boys and girls in separate rooms. No exceptions! Velma: Then I guess I'm with you, Daphne. Greta: I SAID, NO EXCEPTIONS! Velma: But I'm a girl. Greta: Oh... right.
When the Mystery Machine won't start, the gang opens the hood to see what's wrong:
Daphne: Can you see the problem, Fred?
Fred: Well ...*points flashlight* You see that big hole there? That should be an engine.
Shaggy: So, like, those fake gator people are selling fake gator products? Dude! we are dealing with serious irony!
Sheriff Stone ordering the arrest of the gator people, despite acknowledging he has absolutely no jurisdiction.
Episode 3: The Secret of the Ghost Rig
The Xerox machine exploding toner everywhere.
Fred Senior is caught in one of Fred's traps hanging upside over a Shark Pool.
Daphne continuing her mother's boys/food metaphor:
Daphne: But I don't even like meat, I like vegetables *dreamy expression* like Fred.(which, considering Fred's level of intellect in this series, is oddly appropriate)
Scooby tattooed a map of Crystal Cove's resteraunts on his tongue.
Officer: You realize you were speeding?
Man: Yes, officer.
Officer: Okay, as long as you know.
"I wouldn't let anything happen to any of you guys! You're all the same in my eyes."
The completely ridiculous way of getting into the ghost trucker's lair. First you pull the lever, which reveals a little piece of rock with square and triangle shaped holes cut into it. Once you put the correct blocks inside, it reveals an elevated rock that you sit on, which finally opens the gate.
Episode 4: Revenge of the Man Crab
Fred putting the 8-track cartridge on the turntable.
Fred: Why isn't this working!?
Fred trying to comfort Daphne by promising her that he'll never have a feeling again.
Skipper Shelton's exchange with Scooby:
Skipper: Almost doesn't shuck the clam. Does it, Wolfie?
*He and Scooby share a long laugh*
Scooby: I have no idea what you're talking about.
At one point in the episode, a random seagull is pulled under the sand by the Man-Crab. Later in the episode they find the cage where everyone the Man-Crab had captured is, even the random seagull was in there.
"Easy there, Daphne! Remember, we're married. Try not to look so happy!" This may explain why we have yet to see Fred's mom in the series.
Oh this so does, and it isn't pretty. Mayor Jones told Fred that his mom left him while he was a baby...but then we find out Mayor Jones STOLE Fred from his real parents making this Harsher in Hindsight.
The villain at the end explaining how she convinced every kid in town to play along with her scheme:
Que Horrifico: I offered them utopia! (Beat) When that didn't work I offered them candy.
Episode 6: The Legend of Alice May
As Ghost Girl attacks the high school prom.
Shaggy: Like, wow! I didn't know this year's theme was terror and pandemonium!
Velma: What's going on?
Random Kid: Somebody's mom is trying to kill Fred.
For some reason, the way Shaggy has to calm down Velma by saying, "Stop breaking the cemetery!" is pretty funny.
Episode 7: In Fear of the Phantom
Scooby introducing his new best friend - Shaggy's old puppet.
Shaggy fighting with "Harry".
Shaggy: *stops in mid-scuffle* Wait a minute... what am I doing?! You're just a puppet! You can't hurt me!
Fred: Quick, Velma, set your milky whiteness for STUN!
Also, the "Oui, Oui" act.
Episode 12: The Shrieking Madness
Harlan Ellison's lecture ("...and that's why nothing good has been written since the 1970s!") and snapping at Shaggy ("What if "like", like, were used, like, in its proper grammatical form and not, like, a conversational pause, like every third, like word?")
Episode 13: When the Cicada Calls
Episode 14: Mystery Solvers Club State Finals
Captain Caveman: Captain Caveman no read modern ink symbols. Modern ink symbols mock Captain Caveman.
Shaggy: Like, where does she keep getting these weapons? That outfit has no pockets!
Everything about "Dusk" (a TwilightExpy) and its author. From an English professor (Hatecraft, an Ensemble Darkhorse) despairing over how physically attractive guys and romance are now "what matters" in literature to the Stephanie Meyer Expy's entire characterization. Methinks there are members of the TwilightHatedom on the Mystery Incorporated staff.
YMMV, but also the parody of how a lot of universities today are there to make money and not educate people, as shown with the dean.
Continuing from episode 25 having everything about "Dusk" being funny, in the first episode of season 2 the Dusk actor "Baylor Hotner," who couldn't be a more blatant Taylor LautnerExpy if he tried is here as Daphne's perfect boyfriend and the star of a few shirtless scenes including a commercial for jeans.
So the writers clearly have a fondness for Twilight jokes at this point.
Also from that episode, Scooby get all the information he needs to find the others, and right after that, he say, "Got any Scooby Snacks?"
The moment Fred , Scooby and Velma barge into Shaggy's room and see Shaggy and Daphne kissing each other, which renders both Fred and Scooby catatonic. After snapping both Shaggy and Daphne out of it, they can't seem to wake up the other two:
Daphne: What if their minds are permanently gone?
Velma: How could we tell?
Velma's solution? Tell both Fred and Scooby that it's the dream and they snap out of it.
Don Phong...Dean Fenk...Dan Fluunk"
Episode 37: The Midnight Zone
Episode 38: Scarebear
Mr. E: The sheriff refused to arrest the gang. He's a dimwit.
Prof. Pericles: This is not news.
Also the mayor's constant hints to make sure the Sheriff doesn't play the disc implicating the gang and the Sheriff's excuses as to why he's not playing the disc to Mr. E.
When Scarebear suddenly starts talking before being unmasked, and in a Christopher Walken style voice, to boot!
Episode 39: Wrath of the Krampus
Scooby and Shaggy are more intent on prison food than they are on capturing Krampus, though this ends up justified.
The gang are meeting up with someone lifting weights. It's Mary-Ann from Season 1.
Episode 40: Heart of Evil
Shaggy pulled off a great feat of driving completely by accident in "Heart of Evil"
How Dynomutt fights in contrast to his gruff partner.
The contrast in itself between the two is amusing. You have Dynomutt, a standard "wacky animal" character... And a Frank Miller-ized Blue Falcon who spouts off nonsensical statements and always goes with the aggressive approach.
Episode 41: Theater of Doom
The only part of the play we see, which begins with Scooby and Shaggy singing terribly while doing a shuffle in eerie light. What really sells it is that their singing is practically yelling.
George Avacados reaction to Shaggy and Scooby showing Vincent van Ghoul what they can do.
Boss: Back to work, Avacados!
A few seconds later.
Vincent van Ghoul: I'm doomed.
Avacados: Yes you are! Ahahahaha!
Shaggy: You find anything?
Velma: Just a ham in a friar's costume who doesn't want the show to go on.
Shaggy and Scooby look confused for a second, then Scooby holds up a giant ham
Shaggy: You read my mind, buddy! Starts eating again
Episode 42: Aliens Among Us
This little gem occured after Stone finally told the Gang that he was abducted by Greys as a kid after beating around the bush for like, about, half the episode:
Shaggy: So you're saying that you were abducted by aliens.
Velma again dreading to go to her mother for help on the mystery.
Shaggy and Scooby are very susceptible to hypnosis.
Episode 43: The Horrible Herd
Episode 44: Dance of the Undead
Upon learning their going to fight Ska-Zombies, the Hex Girls only have one question: Can they wear their war paint?
The back story behind the criminals will leave you in stitches.
When Sheriff Stone first confronts the dancing zombies at the Tiki Tub.
Sheriff Stone: Freeze! Nobody move a muscle! (zombified people continue to dance) I said freeze! (zombified people still dancing) Oh come on people!
This part with Shaggy:
Shaggy:(over the hospital intercom) Will Dr. Scoobert Dooby Doo please report to the ICU? Dr. Doo to the ICU.
Random Doctor: Please don't play with that.
Shaggy: Heheh... sorry.
Shaggy and Scooby getting way too into the Hex Girls song, especially when they begin demolishing the set.
Shaggy and Scooby's excuses for not being affected by the ska music.
Daphne: Shaggy, Scooby, why isn't it affecting you?
Scooby: I'm a dog. Music is just noise to us.
Shaggy: And, like, you've heard me sing. I'm totally tone deaf!
Shaggy tries to yell to the Hex Girls on stage about their problem, while Scooby Doo unplugs their equipment, leaving everything quiet except for Shaggy, who's yelling that he needs their help to stop zombies from taking over the world.
Everything that has to do with Skipper Shelton in his one minute cameo at the end.
There's something about that ridiculous ska music that just makes this troper laugh.
Episode 45: The Devouring
The montage of Scooby and Shaggy eating all the glutton food in town and progressively becoming fatter.
Dr. Spartan breaking into a mess hall and completely wrecking the place in an attempt to get rid of all the food. Fred joins in.
When Daphne tries to confront Fred about his feeling for her.
Daphne: You know Fred, with everything that's happening, it makes you realize how precious life is. It kinda wants to make you not waste time and just tell certain people how you really feel, doesn't it? I think I'm ready now. I'd be open to hearing how you feel.
Fred: You mean, like, emotions or something crazy like that? Uh... Well, right now I guess kind of...
Fred: Hungry! I feel hungry! (stops the mystery machine at a pizza parlor and runs inside)
Daphne: Hunger is not an emotion, Fred Jones!
Dr. Spartan explaining about the different types of food based demons, and how he could not manage to catch the olive oil demon.
Dr. Spartan: Slippery Devil. Ha!
Episode 46: Stand and Deliver
"Adventures are stupid."
After confronting a man whose wife recently ran off with the Dandy Highway Man.
Sheriff Stone: Sometimes the things I see on this job... they just don't sit right.
Later when he's talking about how they're all men, and they can get through this. Cue the Dandy Highway Man knocking down the door on top of him and stealing Mayor Nettles, leaving the sheriff freaking out.
While all the men are complaining about the Dandy Highway Man stealing their women, one of them randomly shouts "I'm hungry!"
After the Dandy Highwayman robs Daphne's parents:
Daphne's father: I lost her, and I wasn't even trying this time.
Episode 47: The Man in the Mirror
How Brad Chiles as Fake Fred contrasts to the real one.
Fake Fred: Does the dog need walking?
Scooby: I walk myself, Fred.
Fake Fred: Perhaps you would enjoy a canine crumpet?
Scooby: That is not a Scooby Snack, Fred.
Fake Fred: What difference does it make? I'm sure they all taste the same.
Scooby:(turns back to Daphne and Velma and mumbles to himself)
Earlier on in the episode where the gang is investigating the house.
Fred:...Well gang, it looks like we've got another-
Daphne: -Mystery on our hands! Oh Fred, we're such soul mates. We're finishing each other's sentences.
Fred: Come on, let's-
Velma, Shaggy, and Scooby: -Split up and search for clues?
Shaggy: Like I guess that means we're all soul mates!
Episode 48: Nightmare in Red
Velma's complete break down over how nothing makes sense anymore, and she can't understand anything. Sure, she's kind of pitiable at that moment, but you can't help cracking a little smile at how it happens
Velma: ...AND NOVA'S TALKING!!!
Episode 49: Dark Night of the Hunters
Scooby:(referring to the mosquitoes) They bite me, I bite 'em back.
Episode 50: Gates of Gloom
Sheriff Stone throughout the entire episode.
Him trying to explain what's happened while the gang and Mayor Nettles were away.
Sheriff Stone: I'm scaring myself! And I hate it! picks up chair and begins slamming it against the wall I HATE IT! MAKE ME STOP!
"Please Bronson, they're not even whipping you."
At the beginning of the uprising, Sheriff Stone gives a speech on how he must start the uprising because he loves Mayor Nettles. It was pretty heartwarming, and at the same time awesome to see the character give a serious speech. Of course, they had to put one funny line in there somewhere.
Sheriff Stone:... for all the times I arrested the wrong person...
The fact that Professor Pericles actually made his robots take Nova down below in the mines while she's still in her hospital bed. This is addressed during the uprising.
Sheriff Stone: Listen up everybody! Follow me! TO FREEEDOOOM! And will somebody please bring that sweet little dog in a coma? Thank you.
Episode 51: Through the Curtain
Shaggy completely freaking out in the boat when the gang is trapped in an interdemensional sea.
gang sits quietly in the boat for about five seconds
Shaggy: I CAN'T TAKE IT ANYMORE!!!
Episode 52: Come Undone
An insanely morbid one, but, as the Gang are fleeing from the Entity's minions, they run the exact same way they used to whenever they were chased in the original series.
Scooby pleads for Nova to tell him how to defeat the Entity and she responds that he will know in his heart what to do. He responds with a frustrated "Seriously! Just tell me what to do!"
The looks on both Shaggy and Scooby's faces upon seeing the alternate Ricky Owens and Cassidy Williams kissing during a commercial and Professor Pericles—the Big Bad—is their sponsor.
Pericles' happy and goofy tone of voice sells the moment. After spending a whole series being a constant source of Nightmare Fuel, seeing Pericles like this is hilarious.
Sheriff Stone and Mayor Nettles's kids in the alternate timeline. Three sons and one daughter, who can stay up as late as she wants on account of being more adorable than her brothers.