When Amy jumps Silver assuming he's Sonic, Silver's reaction is priceless.
Sonic tossing the holographic device with Eggman's message in it back to Knuckles, who fumbles to catches it with his large mitten hands and drops it on the ground. He proceeds to stomp on it angrily while glaring at Sonic.
Shadow stopping time via Chaos Control, before casually walking behind Silver, mid-dramatic punch, and roundhouse kicking him in the back of the head.
In the last story, during the scene of Elise resurrecting Sonic, look at Silver's face right before the kiss. It's almost as if the guy saw the moment coming.
In the previous cutscene, when the gang splits up to collect the Chaos Emeralds, Knuckles begins to go in the wrong direction before turning around.
After Shadow enters Eggman's base by bursting through the ceiling:
Until the four or five-hundreth time it happens to you, watching Sonic start breakdancing during the Mach Speed sections makes it all worth it.
Mephiles exiting the scene by twirling off screen◊ like a ballerina. Okay, possibly not originally intended by progammers, as it appears the character model sets back to the default pose, but his ears and hand clearly show that Mephiles spun at least 360 degrees before the scene cuts back to Silver and Blaze, who never acknowledge it. Now watch the scene while anticipating the action, and you may get a giggle or two.
Mephiles tripping over his own feet(?) once he picks himself up off the ground after being bounced like a ball after "Mephiles Phase 1" is finished. Even while trying to open a portal to escape, he's still having trouble standing upright after that hit. Almighty Super Being, indeed!
Shadow's reaction to an entirely unremarkable bit at the end of Flame Core. The subtitle renders it as "Ack!", but the sound he makes is something more like "RRRRRRRAGGAHHHaaaa...!"
The cutscene after you defeat the Egg Wyvern. The mech explodes in pieces, Eggman's seat is ejected... and on the way down it hits a piece of debris and start spinning sideways. It's hilarious to watch.
Kung-Fu Jesus: ...so yeah, it is amazing, but not in the right way. Medibot: It's kinda like on those nature shows on PBS. Kung-Fu Jesus: No, it's not. Medibot: Well except, y'know, more trains and less animals. IlluminatusVespucci: Mutual of Omaha presents Oh Fuck, A Bomb!
This moment in the Aquatic Base, when they start playing as Knuckles, and the camera and controls work together to become as unwieldy as possible.
"Great!" "GREAT, THE CAMERA SHAT ITSELF!"
The beginning of Shadow's story — the audio was deleted and they had to redo their commentary... and the dialogue. With the voices of the characters of Metal Gear Solid. Keep in mind that this was recorded AFTER the end of the LP. Also, this:
pokecapn: Hey, Sonic-2006-ites, this is still pokecapn...
IlluminatusVespucci: This is still IlluminatusVespucci.
Kung-Fu Jesus: This is still... poke... capn... ew.
They all start laughing.
Medibot: And this is new and improved, with 50% less fat medibot!
Mephiles' voice near the end of video 19 is nothing short of hilarious, especially when combined with his zombie-like behavior and the sound-effects courtesy of the other goons.
"I'm Mephiles, Mephiles the Dark. And I cut myself, sometimes..."
As the LP nears the end, the fact that only Medibot has gotten a full eight hours sleep at all this whole time starts to catch up with them, and the LP starts to mesh into one long CMoF as they get progressively less coherent.
If it exists, it is an Iblis Trigger. No exceptions.
Their attempts to identify whose fault the game was during the credits.
A scripted sequence launches Shadow a bit too high their first time through, which provided such a big reaction that the video is titled "That was scripted."
One of the contests has viewers coming up with explanations for how Eggman could outrun Sonic before the final boss fight in Sonic the Hedgehog 2. Explanations ranged from Eggman possessing speed bladders with excess fast to being shaped like an ostrich (because ostriches run fast as fuck) to just finally being face-to-face with Sonic for the first time with no death machines between them and running on pure adrenaline.
See here for Funny Moments from this group's other Let's Plays.