Classic Dr. Eggman: Wow... Will I really get that crazy?
During the battle itself, everyone repeatedly nags you with cries of "It looks like a homing shot!" Shadow, on the other hand, says "That's a homing shot!" Nope, it doesn't look like a homing shot, it IS a homing shot!
Classic Sonic's first attempt at an Air Dash in the ending. Modern Sonic does it in an earlier cutscene and Classic Sonic was impressed by it.
In the boss fight against Silver, he piles up a whole shitload of cars and debris to try and crush Sonic. Once he takes the final hit, Silver is immediately squashed by the entire pile.
On the same note, Silver's entire reason for fighting you in the first place if you talk to him as Classic Sonic.
Silver: Sonic, is that you? Or are you just a fake sent for the Chaos Emeralds?
If you're Modern Sonic, the reason goes from that to fighting you Just for Fun, which is oddly appropriate, as his boss fight is genuinely enjoyable.
In Classic Crisis City, four-fifths of the way through the level, you come up to the goalpost... only for the tornado to carry it away, taunting you with it for the rest of the level. One can imagine the trollface plastered onto the tornado when this happens.
The fact that Sega pulled such a trollish stunt with arguably the most polarizing level in the game, given its source, also makes this a slight Crowning Moment of Awesome, just for how ballsy it was.
Also a Crowning Music of Funny... The Super Sonic music starts off with the opening note to Live And Learn... then immediately switches to a remix of the Sonic 4 Invincibility music. Listen for yourself here.
Which is made even funnier when you realise "the door" they're looking for could very well be the door TO THE GAME'S COLLECTION ROOM.
When both Sonics see each other for the first time prior to the Death Egg Robot battle. Both are convinced that they are looking in some sort of fun house mirror and begin making silly poses in perfect unison.
And then when Eggman begins talking, it's Classic Sonic that runs off — while Modern Sonic is so astounded by the fact that it wasn't a mirror, and that it was his past self, that he doesn't move for several seconds and winds up smacking into the door after it closes.
"That pink water makes me really nervous for some reason."
The fact that you can use unlockable music on any stage. Any stage.
In the gallery, the artwork 013 picture. You have a beautiful picture of Sky Sanctuary, expertly coloured. Then you have a rail... and a quick stickman-like doodle of Sonic, complete with arrow showing which way he's grinding.
Classic Planet Wisp, specifically near the start, features the basic "pit with two springs facing each other" obstacle. The funny part comes in the fact that Planet Wisp is the last stage in the game, meaning you've probably stopped expecting it if you ever were before.
Even better in that in the Doppleganger Race, the "time ghost" Sonic actually gets stuck in that pit, albeit briefly.
During the Perfect Chaos boss fight, in phase 2, if you land on a certain platform, Chaos will start charging up a laser, looks like he's about to fire it... and destroys your platform with his tentacle.
The Thunder Shield challenge in Classic City Escape. The GUN Truck is absent... Then you hear it from somewhere. Go on ahead and you will find it trying to drive into a wall.
The cutscene after the Egg Dragoon battle, with Eggman declaring that he was supposed to beat Sonic this time, and Modern Sonic's retort that he always beats Eggman... And then turning to his past self & confirming that yes, they really do beat him every time, which leads to Classic Sonic breaking out in laughter.
In Classic Crisis City. There's a loop that moves the camera to practically behind Sonic as he goes through. It's a blatant reference to a loop in Palmtree Panic from Sonic the Hedgehog CD that has you do the same exact thing. That's right, they make a reference to a game about time travel in a level from a game about time travel.
While other characters just curiously look around once they are freed, Blaze leaps 10 feet into the air and lands gracefully on a pole. Why? No reason.
At the end of the game, when everyone returns to the birthday party to celebrate, Shadow is just standing around awkwardly, like he's only there to be polite. Shadow is also the only one who doesn't wave when Classic Sonic and Classic Tails return to their timeline.
Don't forget the 3DS version. Sonic's response to being told that he's early to his surprise birthday party is to propose running around the world. Everyone will probably be back by the time he gets back. Probably.
The stinger with Modern and Classic Dr. Eggman arguing. Including the latter asking what time it is (For the sake of context, there is no time where they are). Twice. And gets slapped for it the second time.
The last part of the final boss. Both Sonics charge towards the Time Eater; when they're just close enough, it appears to prepare an attack, and they fly straight through its weak point before it can react.
The newly-designed GUN truck. The fact that it featured new adjustments since last time to chase after Sonic, including a rocket boosters to follow him up a side of a building. All just to catch one hedgehog, in an over-the-top Roaring Rampage of Revenge. Only to wind up smacking into an alleyway once Sonic runs through it. The player can see the smoke plumes in the background before making way to the goal.
When you score a successful hit on Metal Sonic, he will bounce off the ground back first, do several flips in the air, hit the ground again, do more flips, then hit the ground again and scrape to a halt like an action figure hitting the ground after being thrown. It's hard to not at least giggle while watching it happen.
Double hilarious because his second to last attack pattern involves a gigantic death ray with a long warmup process. While you're expected to wait out his attack and hit him while he's weak, Sonic can simply jump up and smack Metal Sonic right out of his warmup sequence, which results in Metal Sonic unceremoniously being chucked off screen without any kind sort of fanfare before the next phase.
More on a "what were the censors thinking" level, but the loading screen to the Modern Sonic Rouge friend mission labels her as The Temptress. How this wasn't another Sonic game that went out the door with an E10+, I'm not sure.