He references the famous "When the X is Y juuuuust right" meme in his review for Quirky Unconsistent Incomprehensible Nonsensical Track.
You can find Clown Man in the tier 2 level hub, which is the sewers for the city. When talked to, he'll question why people are afraid of him, saying that "he's not even it or anything". There's also a red balloon floating around in the screen Clown Man is in. Additionally, if you burst said balloon, Clown Man's dialogue changes to "Why so serious, Mega Man?".
Renhoek's Tier X Level "Mario Land" ends with Bowser spitting out a Star, which is the reskinned Energy Element for the level. The way it floats, changes color, and the fanfare bit that plays when collected is a reference to Make a Good Level X specifically.
In fact, his entire boss fight past the first phase is a Kirby's Adventure reference. It even ends with them making the same hole in the moon that Nightmare made.
Additionally, the attack where he splits into two massive electrified spheres is directly lifted from Magolor Soul, complete with the background change.
Haunt Man's laughing sound effect is sampled directly from Shovel Knight's Black Knight.
A Polybius arcade cabinet can be found in the Tier 5 hub. Examining it causes the player character to get motion sickness, as per the legend. Also, if one returns to the cabinet after having examined it, the cabinet is gone, with Fake Man pulling a Move Along, Nothing to See Here, similar to the legend's Conspiracy Theory nature.
The fight against Avoidance Cherry is a shout-out to an I Wanna Be the Guy fan game named I Wanna Touch The Entrance. Fittingly, the song used in it is called... Entrance (from Cytus).
In the entry level "Gunpowder Cellar", Isaac can be found curled up in a fetal position in one of the barrels.
The four top entries from the first MaGMML are represented with statues in Tier 10. Citadel Basement is represented by a statue of a Guts Lift; NEON GRAVITY by its midboss, The Moon; Mega Man World by its boss, Birdo; and Glass Man by Glass Man himself. The latter three all lead to boss fights against the respective characters after clearing the Wily Star.
Talking to Skull Man prompts him to say that travelling with the Hell Wheel is much faster.
The final level in the main game is a giant maze recalling Mega Man's experiences in this game. Once it's beaten and Wily is seemingly cornered, he sets off a Self-Destruct Mechanism that alerts him to escape and disables Mega Man's teleport. Is this MaGMML2 or RM4MI?
The use of the name "Chimerabot" in terms of the bosses of MaGMML2s maze isn't the first time that name has been used: see RM4MIs chimerabots, who were also fusions of previous Robot Masters.
Sakugarne's upgrades make it similar to its appearance in RM4MI where it can be used to pogo on spikes and off of bullets.
Eddie can be killed with Slash Claw for extra powerups, and doing so makes him never appear in levels, similar to in RM4MI where using Recycle Inhaler on him gives you a powerful upgrade but makes him disappear for the rest of the game.
The music for The Arena is Illusion, from F-Zero Climax. RM4MI also had the same track playing for its Boss Rush gamemode.
Behind a fake wall in Tier 1 is an Easter Egg of a section from "Objective: Vain Space" from the first contest. Jumping into the void puts you into an endless fall loop, accompanied by the endless staircase music from Super Mario 64.
Most of the references to Mega Man Eternal (including Eternal!Scorch Man's role as half of the Tier 4 boss fight) may have been removed from the final game at the request of its creator, but Jolt Man still has a cameo as "El Jolto" in some of the Tier 4 subway posters. Also, Tier 1's hub area is based on a modified (and very damaged, buggy and off-color) version of Jolt Man's stage.
If you play through the game with the swear filter enabled, all the uses of the word "Hell" get replaced with "Hello Kitty".
The Plug Man located in the Chateau Chevaleresque is called Shameless Plug Man.
The boss of the "Coyote Man" stage is Wile E. Coyote himself, piloting a Wily Capsule-esque machine that—like in Wile's cartoons—is subject to Self-Damaging Attack Backfire.
The level "Defeat the Giant Spear Man!" is one long love letter to the Wario Land series (except the Virtual Boy game and Shake It!). All of the enemy sprites and environment come from its various games, and the second half of the level is a Timed Mission in the vein of Wario Land 4, complete with a Frog Switch!
Temporal Pillar's time stop gimmick and the way coloured objects interact with stopped time is likely, in conjunction with the boss being Sakuya, a reference to Touhou Luna Nights.
The True Final Boss, the GameStop Duck, starts out wearing the armor of the Lingering Will before bursting out of it to fight. It also uses tricks one would associate with Keyblades to fight.
◊ has him set his house alight before sitting at a table with a mug of tea and proclaim that "This is fine".
