In episode 11 of the Japanese version, Rouge's response to Topaz getting out the handcuffs is "So you're into S&M, huh?"
In one episode, Sonic and Sam Speed race to settle who's the fastest. At first it looks like a photo finish. However, upon looking at the camera footage, it's revealed that Sonic actually finished, jumped over the white tape, posed for the camera, ran back and did the whole race over again.
Just about anything involving the Chaotix.
In their first appearance, Charmy's attempts and ultimate failure to introduce himself before the commercial break.
In the Japanese version, there's this line, also in their first appearance:
The original Japanese line is "Good kids don't stand on moving cars". The absurdity of the advice makes it plain that it's meant to be a parody of Sonic Sez.
Knuckles and Cosmo's brief exchange while the crew are trying to free the Blue Typhoon from a huge maze of what is apparently plantlife - by cutting:
Cosmo: My sister Galaxina and I often did gardening together. It's great therapy. Knuckles: Sure, hacking through deadwood really does it for me, too.
When Knuckles and Hawk are in prison together, Knuckles discovers a hidden microphone. He and Hawk (his inmate) share this exchange:
Hawk: They could change the menu once in a while. I mean, baked beans day in and day out? You'd think they'd never heard of steak, or fried chicken, or even a cheeseburger with fries! (Knuckles takes a deep breath) Now wouldn't that be something?
Knuckles(into the microphone): IT SURE WOULD!!
The Tournament Arc has some funny moments, but the tops would be when Decoe and Bocoe enter...and find themselves fighting each other. The match is called off when the police show up and chase them out of the ring.
"This message has been brought to you by the Eggman Empire, which is not responsible for any of its content. Except this part."
The entirety of Cruise Blues, some examples:
Sonic's plan to get off the yacht and the ways it backfires.
Eggman's various names for his 3 aircraft to please Decoe and Bocoe
Eggman: Rock, Paper, Scissors?
Bocoe:You've gotta be kidding.
The senior citizens petting Sonic like a dog
All of Sonic's panic attacks in the episode, ALL OF THEM.
One that was sadly removed from the dub had Robotnik's Japanese voice actor performing an epicThrow It In and improvising a little rant about how nobody ever dies in shows like this after his minions ask if Sonic will survive his trap. It was so unexpected that all the other voice actors got confused and stumbled through their next lines.
"How To Catch A Hedgehog" is pretty hilarious. A microchip from one of Eggman's robots gets caught in Sonic's ear causing him to run about uncontrollably, unable to stop or slow down. What follows is a Looney Tunes-esque episode in which the gang tries to catch Sonic to find out what's wrong with him. All of their ridiculous traps fail and Sonic continues to just run in circles. The whole time Eggman and his minions are watching and Robotnik's robots are trying to get him to start exercising. It's amazing.
Robotnik: That looks like fun! I think I'm going to start exercising!
Bocoe and Decoe: That's great Doctor.
Robotnik: Tomorrow (starts eating a huge loaf of bread).
Bocoe and Decoe: Tomorrow never comes!
The ridiculous Chatoix Crew plan of getting Tails to save Cosmo; by knocking Knuckles unconscious, drawing a beard on this face, and finally having Espio (while invisible) carry him around and threaten her.
"Even his own mamma wouldn't recognize him", cut to everyone knowing very well that it was Knuckles with makeup during the attempt to threaten Cosmo.
The Sonic X comic basically runs on humor. One particularly memorable issue has Eggman eat one of Bokkun's sugary-treats, which causes him to go hyper and launch into a costume-fueled crime spree, complete with rubber swords. Sonic's strategy for dealing with him? Play a game with Eggman where he has to switch into the disguise of Sonic's choice, which involves Eggman running up and down the stairs of his lair (the costume room is on the top floor), until the doc's hyperactivity wears off. In the process, we get to see Eggman don a plethora of ridiculous costumes, which include a viking, an astronaut, Elvis Presley, a fur-suit, and even a Chris Thorndyke get-up, which disturbs Docoe to no small degree.
There's also the St. Patrick's day issue, where Eggman crashes a St. Patrick's Day parade with a giant leprechaun mecha, looking for a leprechaun to lead him to its pot of gold. Unfortunately, the leprechaun they've tracked is actually Bokkun, who has been accidently covered with green paint.