ROM hacking

ROM hacking is the process of modifying a video game ROM image to alter the game's graphics, dialogue, levels, gameplay, or other elements. This is usually done by technically inclined video game fans to breathe new life into a cherished old game, as a creative outlet, making minor edits to change details or to make essentially new unofficial games using the old game's engine.

ROM hacking is generally accomplished through use of a hex editor (a program for editing non-textual data) and various specialized tools such as tile editors, and game-specific tools which are generally used for editing levels, items, and the like, although more advanced tools such as assemblers and debuggers are occasionally used. Once ready, they are usually distributed on the Internet for others to play on an emulator. There is such a big number of hacks available on the Internet, that searching for Mega Man hacks on YouTube will easily reveal at least a dozen.

Mega Man Ultra
Mega Man Ultra is a ROM hack for the game Mega Man 2 that was developed between 2005-2006 and released on 2006 as an edition to the game. The game features new enemies, music remixes from different games, more difficult levels and different named Special Weapons, although the Robot Masters are still the same, only with a palette swap and different strategies.

Story
''20 years have passed, since the capture of Dr. Wily. During that time period, Dr. Light has been secretly creating a new battle robot called X. Six months ago, Wily escaped, and has stolen the blueprints to create X. Will Megaman find the truth behind Dr. Light and X...''

Notable Differences

 * All the Robot Masters are palette swapped. They also have much more different strategies than the second game, making their battles much more difficult:
 * Metal Man now throws much more Metal Blades (Saw Cutters) when he jumps, and when he goes to the other side of the screen.
 * Air Man shoots the Air Shooter (Top Spinner) faster and does a small hop before jumping twice to the other side of the screen.
 * Bubble Man now shoots more Bubble Leads (Ice Bubbles).
 * Quick Man shoots his Quick Boomerangs (Ultra Beams) faster and dashes twice the faster and twice the times.
 * Crash Man won't stop shooting Crash Bombs (Vector Claws) if he is attacked.
 * Flash Man now runs twice the fast and when he uses the Time Stopper, he shoots more shots than he does in the original game.
 * Heat Man now charges more energy before shooting himself at Mega Man, and shoots himself twice the fast. After that, he may get stuck in a wall, trying to shoot flame blobs but unable to do so, making him very vulnerable to attacks.
 * Wood Man shoots his Leaf Shield faster, it deals more damage, and he jumps to the other side of the screen directly, giving almost no time to be attacked but only in the air.
 * The Wily's Great Temple bosses have also different strategies, and others are also replaced by other bosses, except for Mecha Dragon, Guts-Dozer and the Wily Machine No. 2:
 * Mecha Dragon is now weak to the Bubble Lead (Ice Bubble) and it is the only weapon capable of harming it.
 * The Picopico-kun is replaced by Metroids, and interestingly enough, they are also weak to the same weapon the original boss is weak to: the Bubble Lead (Ice Bubble). This is a reference that in the original game, Metroids are very weak to the Ice Beam.
 * Guts Tank is now weak to the Leaf Shield and now shoots Crash Bombs and Ultra Beams. However, it deals minor contact damage.
 * There are now 10 Boobeam Traps, and they now shoot at intervals. They are also now weaker to the Quick Boomerang (Ultra Beam).
 * The Alien holograph is replaced by a Mega Man, that then transforms into some kind of a jet powered Mega Man that shoots supercharged electrical spheres that spin and now deal slightly more damage.
 * Many enemies are ripped from other Mega Man games and programmed to do what the normal enemies do, the only exception being Wood Man, who has the Super Mario Bros. baddies as the enemies on his stage. The other enemies are also back but others are also palette swapped.
 * The position of the bonuses and the levels is very different.

Bosses
Robot Masters

Wily's Great Temple Bosses

Trivia

 * It is implied that Mega Man kills Dr. Wily in the game, as when the game is cleared, a robot (maybe X) is piloting the Alien holograph, and Wily does not appear anymore in the game.
 * Some enemies come from other games.

Rockman 4 Minus Infinity
Rockman 4 Minus Infinity, Rockman 4 MI for short, is a ROM hack of Mega Man 4 made by Puresabe.

Notable Differences

 * The Jumbig takes a heckuva lot of damage to kill, and occasionally, it launches very fast towards Mega Man, pushing him back once he is hit. But he leaves out a lot of goods when he is defeated. Starting in the Cossack Stages, he is armed with missiles.
 * You can't select Rush Jet, however it does appear in Cossack Stage 1 once Shadow Man blows up your balloon.
 * In Pharaoh Man's stages, Mega Man gets cursed. Depending on the curse, he'll fire rapidly, change weapons, run rapidly, even reverse the player's controls.
 * Half of the Robot Masters have a critical ability that once their health is down. This gives them more speed and extra damage to the player. The music also becomes faster paced.
 * Most of the Weapons are changed in different functions. For example, Skull Man's weapon is called the Hell Wheel instead of Skull Barrier, and instead of sending out mini-skulls to kill enemies it allows the player to move twice faster and he can dodge almost any straight shot.
 * The Air Baloon is now permanent and can be used both vertically and horizontally (basically it replaces the Rush Jet), however it drains your energy instead of costing certain amount of it when it appears. The Wire has also a function which allows Megaman to cling to walls.
 * You can now use Energy containers as storage tanks which do not disappear after you use them and replenish every time you pick up additional health when the main bar is already full. However there are only 4 containers in the game now (instead of 6 + 4 sometimes dropped by Eddie)
 * The Boss Rush stage in Wily 3 is a lot different than other Megaman games. In fact, you now have to browse through 8 constantlly changing environment within the same level in order to find the Bosses, and the teleport capsules only appear there to return Megaman back to start.
 * There's a secret final boss and stage after you beat the Wily Machine. To do this, the player must activate the Wish Star when Wily Machine's health is only 1 bar left. (This also shows the true ending after you defeat the "true" final boss).
 * Killing Eddie in the game with the Reycle Inhaler (Dust) will make him disappear for the rest of the game and he'll be replaced by a grey Eddie.
 * When refighting the Robot Masters, if you kill ToadMan with his own weapon (Toad), he'll turn into a small frog and leaves an orb to be collect. (However, you shall not kill ToadMan in this state if you want to get some bonus points)
 * No matter what stage you choose, the level is ALWAYS difficult. ToadMan's stage and the rest are changed and upgraded into a complicated but challenging design.
 * The stage themes are taken from a lot of games past to present, such as Kirby 64, Mario Kart, ActRaiser, Gradius, Adventure Island, and even obscure Japan-exclusive games like Hokkaido Serial Murders: Okhotsk Vanishes.
 * Some enemies from Megaman 7-10 appeared in their 8-bit style features for the stages
 * Some Robot Masters (from MM1 - MM3) returned in this game. One is ShadowMan while the rest are combined into 3 ChimeraBots (although, there are some make cameo appearances in Wily Stage 3). Megaman will face Shadowman four times in the game, and, upon beating him the last time, you recieve a weapon upgrade to the Rush Coil which, if you have at least 8 bars of energy (half), will get Megaman out of pits if he falls in them, but only once per life or per level though. The upgrade also allows you to take 1 damage from spikes instead of dying, but also only once per level. Basically, it just turns the sprite invincible, like when you've just been hit.
 * Many enemies and bosses are re-modeled in this game, like the Yellow Devil MK-II and Copy Megaman.
 * A lot of Engrish!

References:
 * The Mega Man Network
 * Destructoid