The scene in Sonic Universe Issue 18 where Antoine - while trying to escape from the Battle Bird Armada's island fortress - opens an escape hatch, only to find it opens up onto the edge of a cliff.
"WHO PUTS A DOOR LIKE ZAT IN A PLACE LIKE ZIS?!"
In the same issue, just to prove that no one will EVER forget the margarine scene from Sonic Sat AM - just as Tails is starting to get his rescue plan into action, unaware that Antoine and Bunnie are forging their own plans, we suddenly cut to this:
Random Bird Mook: And then, I dunno, I guess I'd use a bit of margarine!
Antoine: Ah, well, you see, zat is ze problem right there! Eet must be butter!
Random Bird Mook: Really? That makes a difference?
Antoine: A difference? Ha! Zat is like asking if there is a difference between ze water in your glass and zat which is in ze commode!
Tails: You can't stop us, Doctor foo... foo-foo...
And there's Shadow's reaction when Marine tells him that she doesn't know as much about ship building as she let on previously. For several panels, Shadow's expression locks up in one of the most amusing reactions given from a character in the comic
Also from issue #205: when Tails disables the still-quite-mad Eggman's tortoise-bot, Sonic tries to convince him to come back with them. Eggman then proceeds to spontaneously punch him in the face.
Sonic's reaction when Ixis Naugus goes flying through the air while cackling to attack the new Death Egg in issue 225:
"It's got to be an act. Nobody can be that creepy."
In 220, after Feist explains that he didn't stop Geoffrey from double-crossing Sonic because he found it amusing. Sonic replies that it wasn't a problem, then adds under his breath "You creepy, overbearing, ill-tempered, bad-humored, egotistical, badger-panda-giant thing!"
Mephiles: (to Void) Dude, that guy really needs to lighten up.
The following issue, with creepy Flying Frog, leaving Scourge to comment that he makes Rosy look cuddly.
As Silver tries to fight Enerjak in an alternate past in SU 27 he tries think about what kind of advice his mentors would give him. Cue visions of his mentor and Edmund.
Vision of Edmund: Get up you lazy cuss! Kid's today, honestly...
Vision of Silver's Mentor: Your power is your spirit, and thus the power lives in you.
Silver: Great. Either cranky or cryptic.
The framing device in one Sonic Kids story is present-Sonic telling a bunch of kids how Tails got his sneakers. After the story, which involved stopping Robotnik from using a time-stopping device on the forest, Sonic discovers that kids fell asleep!
Sonic Universe issue 37 has a few gems, including Lien-Da complaining about being teleported along with the other Grandmasters, despite being right down the hall from the conference room, and Eggman realizing that Orbot and Cubot have been serving tea and snacks while he's been monologuing.
Even better when Orbot and Cubot ruin Eggman's speech about having complete control over them by handing out tea and cookies to everyone. Including the cyborg ninja queen.
Some of the Off Panel comics. For example, Mecha Sonic marrying Mecha Sally, with Sonic screaming for another universe reboot. Even funnier when, in a later issue, a fan-submitted comic follows the same events, but with Sonic roboticising himself for Sally.
The majority of 195. As the battle against Scourge continues, more and more hedgehogs start showing up, each time spurring another hilarious moment, starting with Shadow.
Sonic (Explaining the situation to Shadow): He (Scourge) conquered this world and then tried to invade Mobius. Since you're here, do you want to help beat him up?
Scourge: Dude! Weak!
A new Metal Sonic then appears to even the sides, then Rob and Silver appear and Amy brings her fight with Rosy over. Mass chaos ensues. All the while, Silver is trying to figure out which one is Sonic. Since everyone is busy fighting, he grows increasingly irritated and eventually holds everyone in place, demanding to know which one is Sonic.
Silver: I've journeyed from the future to find this "Sonic" and destroy him.
Sonic and Scourge (pointing at each other): He is.
Scourge: You coward.
Sonic: Okay, it's a technicality, but still...
Cream's outburst when Team Hooligan has Cheese in SU #22.
Cream: You put Cheese down this instant! How dare you kidnap Cheese! Don't hold him by the wings like that! Do you know how sensitive they are? And give back Ms.Blaze's Sol Emerald! We have worked very hard to get that back for her, you know! This whole day has been nothing but rough-housing and rude people and I simply will not tolerate it!
Nack: Criminy, kid...
The string of misfortunes Larry causes in SU #44 to keep the council from ratifying the new constitution under Nagus' influence. Hamlin's reactions alone sell it.
From way back, issue #119 has Rotor trying to hack Nicole's system to discover her origins (Future Rotor, incidentally). Entirely through monitor displays:
Rotor: Where did you come from?
Nicole: Not gonna happen.
Rotor: Who designed you?
Nicole: Sorry, try again.
Rotor: Awwww... Come on, Nicole.
Nicole: *XP face*
Then at the end of the comic, Nicole's security inspires Rotor to upgrade his own...
Eggman: Do I gain access to that lunkhead Rotor's computer database in Knothole Village? Of course not! His security system isn't just an ego smasher... *shows his monitor with Nicole's XP face* ...it's downright rude!
In the promotional comic for Sonic and All-Stars Racing Transformed, as Eggman announces his threats to each of the other racers (destroying Sonic, taking control of the moonstones, etc) he turns to Beat and tells him that his evil plan for Tokyo-to is... to bring order to it and keep gangs off the streets.
As well as turn Aiai's banana horde into smoothies for himself.
And as they race, when Eggman's missiles destroy the bridge:
On the final page of Sonic The Hedgehog #247, the Genesis Wave gets used again, setting up the Crossover with Mega Man. The "Off Panel" cartoon riffs on it. Standing by a sign reading "Crossover Next Exit", Silver is embarrassed as Sonic remarks, "COME ON! A GENESIS WAVE AND SALLY CLIFFHANGER AGAIN!". Dr. Eggman is carrying Mecha-Sally and sticking out his tongue saying "Nether-Nether-Nether."
The "Off Panel" for Sonic Universe #52 has Sonic and Mega Man preparing to face down the Genesis Unit from Mega Man: The Wily Wars. Sonic kinda snaps at the mentioning of the Genesis.
Sonic: "The Console Wars are never over! This is for the Saturn! Remember the Dreamcast!"
Mega Man: "Aah! Cut it out! I'm multi-platform!"
This line from Sonic Universe #22 where Blaze just forced Team Hooligan to crash:
Bean: ""Like candy from a baby," you said. What nursery did you come from, pal?!"
The cover of Sonic Universe #23. Cream and Cheese dressed up like tough bikers is funny enough, but Shadow facepalming in the background just sells it.
In Sonic #252, Sonic's busy trying to understand how he's back in New Mobotropolis with Tails Doll's monstrous form attacking. When Sonic mentions rescuing Sally on the Death Egg and Tails counters with rescuing King Acorn, the footnote responds "STH#... wait a minute..."
The Off-Panel comic in the same issue. Sonic is relieved to get back to his storyline, realizes he's coming back to King Naugus, Mecha Sally, coma-ed Antoine and an uncertain fated Bunnie... and quickly decides to call Rock back to go stay at his house for the rest of the issue.
The "Off Panel" for Sonic #254. Sonic has another memory restored... and he remembers he left the iron on.
Additionally from 254, Eggman busting through the GUN aircraft carrier on a cobbled together Egg Walker in a manner identical to the Weapons Bed stage from Sonic Adventure 2. What makes it a moment of funny instead of just awesome is that he finishes the nostalgic scene by quoting his A-Rank statement from said game to Orbot and Cubot.
Eggman: "And now you know why I am the best!"
The "Off Panel" for Sonic #258 and Professor Pickle's love interest being MAMA ROBOTNIK