* 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 purple Up'N'Down enemies 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.