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/Boost in the ending. Modern Sonic does it in an earlier cutscene and Classic Sonic was impressed by it.
On the same note, Silver's entire reason for fighting you in the first place if you talk to him before the Rival Battle.
Silver: Sonic, is that you? Or are you just a fake sent for the Chaos Emeralds?
On subsequent attempts, however, the reason goes from that to fighting you Just for Fun, which is oddly appropriate, as his boss fight is genuinely enjoyable.
The fact that damn fourth Chaos Emerald is guarded by Shadow.
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 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.
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.
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 and 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 that is a reference to another game about time travel... and to top it all off, it happens in 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 newly-designed GUN truck. The fact that it featured new adjustments since last time to chase after Sonic, including 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 their way to the goal.
In Act 1, the truck recklessly plows through countless buildings just to catch Classic Sonic, and ends up flipping onto its side as a result of damaging itself from all the hard concrete and metal structures it ran into. Evidently, it got its Act 2 upgrades because it needed such extensive repairs after Act 1 that GUN figured "Eh, why not."
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.
Doubly hilarious because his second 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 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+, we're not sure.
During the credits, the characters that appeared in the game all run across the bottom of the screen in a chibi art style. Strangely enough, Silver is nowhere in the line... He's actually far behind the group, desperately trying to keep up.
When you get a Red Star Ring in Chemical Plant Zone, go talk to Amy, and she will say this:
Amy: You got me a RING?! Aw, it's a Red Star Ring. Not the kind of ring I was hoping for.
Midway through the Reveal Trailer for Sonic X Shadow Generations, part of the CG teaser trailer for the original Generations is shown with Modern Sonic jumping off a ramp and being joined by his Classic counterpart... and then it takes a hard right turn away from the original trailer, as Shadow leaps between them in the opposite direction. While Modern Sonic is merely surprised by his Dynamic Entry, poor Classic looks utterly befuddled at the presence of the dark doppelganger he's completely unfamiliar with at this point in his life.
