The first Mega Man game began life as a licensed game for Astro Boy. Rock himself looks suspiciously similar to Atom during the first game's ending.
The implementation of Rush was inspired by Casshern's robot dog, Friender
Speaking of Friender, that's the original Japanese names of the fire-breathing robot dog enemies in Wood Man's stage in Mega Man 2.
In Mega Man 7, hold the B button when entering the Shade Man stage for the first time, and the music will change to a remix of the music from the first level of Ghosts N Goblins.
Mega Man 9 features a shout out to the original in Dr. Wily's Swiss Bank Account number (19-871-217). December 17th of 1987 is the release date of that game.
How about Chun-Li's cameo as a news reporter in the intro?
Another shout out appears in The Wily Wars for the Sega Genesis, to of all things Sonic the Hedgehog. During the outside portions of Mega Water S's stage, a green, grassy island with waterfalls can be seen in the distance, which bears a suspicious resemblance to Green Hill Zone from the first Sonic game. More blatantly, you have the bosses (referred to as the "Genesis Unit" in later Capcom materials) of the Wily Tower section themselves, Hyper Storm H, Buster Rod G, and Mega Water S, who are a combined shout out to Journey to the West.
Starting from the fourth game, Mega Man Battle Network also had a close relationship with Boktai, from optional quests in the Battle Network game to actual crossover mini-games obtained by linking the Battle Network game with the Boktai game. This material was stripped from the US translation of Battle Network 6 after the relative flop of the Boktai games in the US, leading to fan outcry (to give you a scope — two secret chips, six Navi (summon) chips, an optional boss, and an semi-secret area with accompanying Side Quest were cut out of the game).
After a certain plot event in Mega Man Battle Network 4, a visit to the haunted house in the real world results in a meeting with a stubble-bearded man with a sun-themed bandanna, who gives the player the code for the Battle Chip "Gun Del Sol EX". The man is actually intended to be Hideo Kojima, creator of the Boktai series (and the Metal Gear series, hence the impromptu Solid Snake cosplay), where the Gun Del Sol functions as the main character's weapon.
Mega Man Star Force has an Easter Egg where if you put a Mega Man Battle Network cartridge into the GBA slot, then an event with MegaMan.EXE would occur. Complete with Time Travel (Star Force is 200 years after Battle Network).
In Mega Man Star Force 3, Geo's class has pet earthworms. The name of Geo's earthworm is James.
Fans have noted that the wing bits on the Black Ace form from Mega Man Star Force 3 superficially resemble those of the Freedom, and during its Limit Break attack, it sprouts energy wings that are identical to those found on the Destiny.
And in that same movie, Sigma is voiced by Master Asia.
The Street FighterEaster Eggs in the first two Mega Man X games. X could get the Hadouken (MMX) and Shoryuken (X2) from a gi-clad Dr. Light by performing certain feats. These move were executed the same as in their game of origin (with Fire substituting for Punch), and could kill anything in one hit. X had to be at full power to use them.
Then there's Magma Dragoon, who wears humongous prayer beads around his neck, has a "tien" symbol on his body, can perform the Hadouken, Shoryuken, and Tenma Kuujin Kyaku, and did some pretty questionable things just to fight X. Why hello there, Akuma.
He can also fire his projectiles both high and low, not unlike Sagat.
In X8, Burn Rooster's Enkoukyaku also mimics Akuma's Tenma Kuujin Kyaku, whereas Avalanche Yeti can unleash a Shoryuken after burrowing in the snow. In the same game, equipping the K-Knuckle turns Zero's (or Layer's) Enkoujin and Hyouryuushou (techniques gained from the aforementioned bosses) into these same moves (albeit with the respective bosses' elemental affinities), and additionally replaces Rasetsusen (obtained from Dark Mantis) with Senpuukyaku, a stationary version of the Tatsumaki Senpukyaku. X can also perform the Shoryuken if he has the Ultimate Armor equipped.
The comic book "Emerald-Spears" is one to the cartoon, which was produced by Ruby-Spears.