* Bright Man has an attack similar to Protectos the Goreroid from ''VideoGame/MegaManZX'', where he launches a powerful explosive towards the wall. To avoid the resulting attack, you have to stand in Bright Man's shadow, similar to the way you had to avoid Protectos' nuke.
** This attack also bears similarity to the Lunar Eclipse attack used by Mr. Shine and Mr. Bright from ''VideoGame/{{Kirby}}'s Dream Land 2'', where you had to stand in Mr. Bright's shadow to avoid getting fried.
** Spark. Manbow ''is'' Kine's Spark ability from the same game.
*** If the name "Spark Manbow" sounds odd for a weapon that basically consists of firing light bulbs, it's because it's a reference to the ''VideoGame/MegaManX1'' boss, Spark Man''drill''.
*** "Manbow" is also pronounced similarly to the Japanese name of the ocean sunfish, the same species as Kine.
* There is an {{Homage}} to the [[VideoGame/SonicTheHedgehog1 Labyrinth Zone]] in Toad Man's level.
** If Toad Man hits Mega Man with Toad Spell, he turns into a frog from ''VideoGame/ForTheFrogTheBellTolls''.
*** To further cement in the reference, Toad Man's stage theme is the overworld theme from that game.
** When Mega Man uses Toad Spell, the stars from the casting animation from the NES version of ''VideoGame/FinalFantasyIII'' surround him.
** The Wish Star Adapter, Rush Search and Rush Cannon are homages to [[VideoGame/FinalFantasyVIII Rinoa]]'s {{limit break}}s.
* The Trio of Ring-Rings in Ring Man's stage have the same AI patterns as [[VideoGame/{{Kirby}} Lalala and Lololo]].
* The way to unlock the secret path to Wave Man in Dive Man's stage looks a lot like Samus using the Power Bomb to unlock [[VideoGame/{{Super Metroid}} Maridia]].
* The [[VideoGame/{{Gradius}} Cube Rush]] shows up as the last challenge before the {{boss battle}} in Dust Man's stage.
** Using Recycle Inhaler on the Up'N'Down enemies in Pharaoh Man's stage causes them to give chase to Mega Man for a while before exploding, in a similar fashion to the Scarfy enemy from the VideoGame/{{Kirby}} series.
* Shadow Man uses [[VideoGame/FinalFantasyIV Edge]]'s {{Ninj|a}}utsu skills (Katon, Suijin, and Raijin) in Pharaoh Man's stage.
* Hell Wheel is basically VideoGame/{{Kirby}}'s Wheel ability. [[spoiler:The very end of the game completes the reference.]]
* The sprite for the Wire power-up on the weapon select screen is the [[Franchise/TheLegendOfZelda Hookshot]].
* Upon defeating an end of stage boss, a victory ditty from the ''Franchise/{{Pokemon}}'' series is played.
* Square Machine uses an attack pattern very similar to [[VideoGame/MegaManX2 Serges]]. It's even ''called'' the Serges Devil Machine. The Aqua Devil fight has some elements to the Agile fight in the same game (to a much lesser degree).
* Nightmare Suzy is based on Nightmare Mother from ''VideoGame/{{Mega Man X}}6''.
* In its final phase, the boss (as a single eye) surrounds itself with four bubbles, making it resemble the VideoGame/{{Kirby}} boss Kracko Jr. Before that, it also drops blocks in the same formation as ''VideoGame/{{Tetris}}''.
* In the second half of Wily Stage 1, Mega Man can hijack a Sniper Armor, an Apache Joe Chopper, Gunner Joe spacecraft, and a Cannon Joe cannon. All of this is based on the Ride Chaser and Ride Armor sequences from ''VideoGame/MegaManX''.
* The AutoScrolling second half of Wily Stage 2 is based on the high speed zones from the ''VideoGame/{{Gradius}}'' series.
* [[spoiler:Shadow Man]] as the BonusBoss of Wily Stage 4 pulls his moves et from [[spoiler:the Ninja ability from ''VideoGame/KirbySuperStar'' and Phantom from the first ''VideoGame/MegaManZero'' game.]]
* The AutoScrolling section of Wily's last stage is based off of the Halberd destruction sequence from ''[[VideoGame/KirbySuperStar Revenge of Meta Knight]]''. It even uses the same music.
** To complete the reference, Mega Man uses Hell Wheel (a decidedly Wheel-esque power) for this section.
* [[spoiler: The section after Wily Capsule Boss Fight]] is based the [[spoiler: organic final level]] of ''VideoGame/{{Gradius}} 2''.
* [[spoiler: The Wily Buster]] is basically Samus's [[spoiler:Hyper Beam]] from ''VideoGame/SuperMetroid''.
* The credits have the theme of Franchise/FireEmblem. Like in that game's credits, it counts the combined amount of times the unit (or in this case, boss), won and lost a fight.
** When you do a critical hit with any weapon, the damage is triple the usual amount. In the Fire Emblem series, any attack with a critical hit gets a multiplier of 3.
* One type of Up'N'Down, according to the credits, is named [[VideoGame/DigDug Dig'N'Dugn]].
* The Mechanical Arena is basically The Arena from ''VideoGame/KirbySuperStar'', with four health pickups in the hub area.
** It tends to be more like "Helper to Hero" from the DS remake as the bosses are fought in a pre-determined order (The Robot Masters are fought in order of their DWN), and mini-bosses aren't fought.
** As of the 0.97 release, it has the TRUE Arena, which likewise based on the remake of ''VideoGame/KirbySuperStar''. This arena ''does'' have randomized matches.
*** One boss in the True Mechanical Arena is Green Helmet, a green Met not seen anywhere else. It has more health than regular Mets, but can be defeated with just one use of the Recycle Inhale, just like the Arena Waddle Dee from Kirby Super Star.