"Kalinka" shows up in the Hub Level...or rather, Concrete Man wearing a costume of her.
The music in NEON GRAVITY being an 8-bit version of "Take on Me" by A Ha can be this for those who aren't expecting it.
Exclusive to Remastered: the Shadow Gacha boss. A gachapon robot designed like Shadow the Hedgehog that uses his sound bytes.
The remix of City War in the final stage. In the original, Mega Man falls through the floor repeatedly, finally landing next to the target he has to take out. In Remastered, one point shows an Illusian creating fake ground, and invisible ladders have a Jamacy climbing on them. Either way, it’s basically a Take That! to the glitchiness of the original.
Cheat Man will shoot the text box words down at Mega Man when the fight starts. The funny part is seeing some of the special dialogue (Bass gets arrogant about defeating Cheat Man, while CX is full of Dull Surprise), most of which ends in some variant of AGGHGAHGAHH when the word bullets start raining down.
First few rooms: Mega Man's on a space ship and Dr. Light is telling him to take control of it. You progress forward and find a Whopper enemy that you'll probably go and kill because that's what you normally do to midbosses, right? Turns out that the Whopper is the power source of the ship. Destroying it blows up the shuttle and sends Mega Man down to the asteroid, with Dr. Light berating him for it. What's better is that, after seeing Light's sass about not destroying the reactor core, you might notice the door behind the Whopper on a second playthrough. Enter it, and you can pilot the ship, just ending the level then and there.
Even better is Dr. Light's warning that Wily probably has his strongest robots guarding the bridge. Since the Whopper is actually the ship's power core, it doesn't count. So what has Wily sent to guard the ship? A single, slow moving, easy-to-kill Tom Boy. Yeah.
Throughout the level, you'll find those One-Hit Kill drills from Napalm Man's stage. Once you reach the mid-stage checkpoint, you'll find Eddie present there to drop you a powerup. Except not: he'll instead deposit one of the giant instant death drills right in your face.
What's better is that, if you avoid the drill, then head into the hole created by that drill, there's a second Eddie there who drops an actual item. It's a Yasichi reskinned as Gutsman's Ass, with the accompanying sound effect.
Near the level's entrance, Guts Man comments that coming up with a good joke relating to it is a pain in the asteroid. Oh, Guts Man.
Seeing Air Man dab in MrKyurem's level is pretty hilarious.
Wily tears open a portal in space to unleash the game's penultimate boss: megaman from Megaman Sprite Comic. Who promptly turns against Wily and fights Mega Man anyway for being a "rubbish ripoff" of him.
megaman: i don't take orders from assholes. go away [proceeds to knock Wily off-screen using a basketball]
In Zieldak's Tier X Level "Metallic Ocean", the secret second energy element is guarded by another Joe Man. After filling up 10 health bars, he instantly explodes and drops the Energy Element. Considering the reception to Joe Man R, this is clear Self-Deprecation.
The True Final Boss battle against Absolute Zero starts off very serious, but as you take down each phase, he gets increasingly verbose and starts becoming much weaker. By the fourth phase, he's just as much of an Anti-Climax Boss as the original Zero fight, and just as ridiculous.
While wearing the Rush costume, the replacement for Rush Jet is Mega Man himself, not looking amused. Not so fun now, is it?
One of the bosses in Null and Void is... a bee. That's literally it. Its only "attack" is to endlessly home in on you. For even more hilarity, Hornet Chaser one shots it. In the Dojo, it's labelled as "Literally Just a Bee".
This exchange before the Tier 8 boss battle begins.
Meeting Gordon Freeman in the Tier 2 sewers would already be pretty unexpected for a Mega Man game, but then he suddenly starts singing you “the song of his people”.
A Meta Example in the Tier X level "Hardcore Parkour"; The boss at the end, an upgraded Toad Man, has a glitch where, if you lose to him, he dies as you respawn. This is a glitch that has been around for a while, but no one seems to be able to fix it. In other words, the dev team can't keep Toad Man from losing, even when upgraded to final boss levels of difficult!
If you set the Text Content to family, the word "Hell" gets filtered into "Hello Kitty". This leads to hilarity such as Door Man darning you to "Silicon Hello Kitty" and Skull Man boasting about travelling with "Hello Kitty Wheel". It also changes the name of one level to "But It Lacked the Depth to Convince Me That This is Really Hello Kitty".
The Tier X level "Mario Land" was fairly divisive (for forcing players to suddenly have to play as Mario, as well as a super-difficult boss on the "secret" path). However, the end of the "normal" path has a couple of funny moments. First, there's a fight against Dr. Wily in Bowser's clown copter. Then, when you beat that boss, the fight turns out to be a hologram, a la Mega Man 2, with Bowser at the controls of the hologram generator.
From Episode Zero
The boss fight of Lily Airpad. Toad Man, after repeatedly asking Zero to stop tearing up the stage lest Toad Man continue to be seen as a joke, seems ready for an epic battle set to some dramatic Shovel Knight music... only for him to die in one shot from any weapon.
Toad Man's surprise appearance in Bubble Base is also a moment as well.
One boss, Mega Man 2 NETA, is a reference to a meme and has you fight all eight Mega Man 2 Robot Masters at the same time. Sounds difficult? Well, the thing is... they all die in one hit thanks to Zero being under the influence of a Super Star. Even better is the phone call with Yamato Man, who starts freaking out when Zero goes into full A God Am I mode.
The Robot Master museum features a screen showing Wily kneeling and pleading before Mega Man, and looking at the screen shows his many, many defeats with that same animation (at one point being switched out for Quint and Justice Man).
the OwO face of the Wily Star."I feel like I'm being subtly insulted."