The music for when you get a new weapon is made of awesome. MM3just says, "I have a new power, and I'm coming to kick ass!"
The original weapon get theme is more awesome than not just any of its remixes, but any other weapon get theme in the entire series. In fact, said theme was so awesome, it was brought back as the US opening theme for X5 (it kicks in at 0:15).
U-GEN's remix of Blizzard Man. Also, there's a number of interesting remixes which have themed instruments based on where the robot masters actually came from—here's the link for Tomahawk Man, you can follow the links to the others.
King of Blades, the song for Blade Man's stage. It might not seem all that great to some people, as it feels like an 8-bit theme based upon a much higher-resolution soundtrack, but arrangements seem to fix this problem nicely.
Both intro stages sound great, but X's stands out in particular. Nothing better for getting you pumped up for an action-packed sci-fi platformer.
Zero's Theme, as opposed to his previous themes, suddenly gets an air of mystery and "more challenges I shall inevitably face" atmosphere around it. This music declares that Zero is officially The Stoic.
Mega Man X6
Say anything you want about X6. Insult it all you like. But you must concede the music was awesome. Personal favorite: Infinity Mijinion.
Speaking of Mijinion, Breis remixed it, it's a pretty awesome track.
Another iconic theme for this series that needs to be mentioned is X, The Legend, as well as its other version, The End of Legend used only in Zero 1 when you defeat Copy X. Combine it with Copy X's broken apart body and the scene borders on terrifying.
The ending theme of Zero 3, Everlasting Red, or the vocal version by Zero's seiyuu, Everlasting. What makes the vocal version even better is the final lines (in lovely Gratuitous English that doesn't sound bad at all): "Welcome the new world, no need to fight....goodbye, yesterday, with all of my heart..."
Be Somewhere - Game Edit The anime and the games usually remain separate from each other, both in continuity and in music. But the opening theme for Stream was so awesome that they added it as the opening for the DS version of EXE 5.
Not strictly a Star Force song, but used in the advertising for SF 3, Stellar, by Kick Chop Busters (KCB).
Sometimes, when you enter an area as Mega Man in Star Force 3, the music changes to something sinister in order to alarm you about a lurking Omega Boss, aka superpowered Bosses from the other games of the series, regardless of where you are in the story. This particular music also overrides the normal battle theme, so you won't forget about the danger lurking somewhere on the Wave Road. This means that you could encounter someone crazy like Wolf Forest right at the beginning of the game. Way stronger than usual. The music in question is here.
Street Fighter X Mega Man
While it is hotly debated whether Street Fighter X Mega Man is a "real" Mega Man game, it's agreed unanimously that the music, composed and remixed by A_Rival, has the same awesomeness as the rest of the games, and captures the feel of both series. Hell, it even mixes some original Mega Man tunes with the Street Fighter themes.
Do you know what it's like to be built this way / With only the power to push others away?
The best part of that song was Wily's ultimatum partway through.
Up in the sky / ten miles high / A man stands above the city he will destroy.
Built from airplane parts / his propeller spins as he thinks to himself / "I will destroy these people."
(And I will fly high above Monsteropolis / and I will rain terror down on the general populace.)
"For If I can't walk among them / then I will walk this world alone."
There will be a fire in the sky / And your doom will rain down!
Built from pieces of SR-71s! / and planes that crashed in World War II! / There will be a tombstone with the Planet Earth engraved on it!!
Also, Man on Fire (Heat Man) [You are the hero! / I am the fire! / This is the meltdown! / Of your desire! / Your fight for justice turns to ashes / Meeegaaa Maaan!], Metal Dance (Metal Man)[You want to fight and try to be the one to bring me down / But I know that there's no chaaaance! / And I know, as soon as you step foot inside that door / You'll fall victim to my metal daaaance!], The Quick and The Blue (Quick Man) [Quick on the draw / in this town, I am the law! / Is what they say true? / Does death wear blue? / Can he faaaalll?]...actually, they are all unbelievably awesome.
They've just released a 4track CD based off of Mega Man 1. Their Elec Man song, 'Evolution of Circuitry', can be found on their Facebook.
Making Wily into a sympathetic, though not blameless, figure is no mean feat, and yet "Look What You've Done" manages it.
And who is this you send? One of them? While you cower, far from harm. He'll just disappoint you. Now it's done / We're divided / Call him home / This one's misguided. I see his hands, covered in my children's blood. And his eyes do not waver. Call me wrong? / The future needs us / Your answer's death? / You end us, bleed us And how quick you had him dispatch his brothers. You call this murderer a savior.
Random, aka Mega Ran, is a rapper who does (among other things) rap remixes of Mega Man tunes. They can be pretty hit or miss, but one of them is certified Awesome: Splash Woman. (The MP3 is available here.)
Thought I was in love before But I love you more, so baby, come aboard And go away with me, so I can make you see What you mean to me, and baby, we can be free... Under the sea Just you and me
And guess what? He collaborated in a song with none other than The Megas.
Hyadain2525 from Japan gives us some...interesting Alternate Character Interpretation of the Mega Man 2 Robot Masters. Some of them are really well made with some neat Easter Egg sound effects incorporated in the songs. All of them (except Crash Man being the first one made) have a little throwback refrain to the song of the robot master that is effective against them. Also they're all love songs:
Trinitro Man (Fun fact - he was originally Nitro Man, after nitroglycerin. However, when Mega Man 10 was released with a totally different Nitro Man as a boss, he was renamed Trinitro Man - as in trinitrotoluene, or TNT.)
In Mega Man Rocks! there are a few good examples: Anchor Man, whose level is ship-based, and Hit Man, whose level is city skyline based along with Police Man who has a stage which appears to be half death trap half robot-police training center.
Also the Doujin game of Rockmen R: Dr. Wily's Counterattack - Demo - Intro Stage and although you may have to look for a Lets Play version Laserman's level, Weasleman's level, and Wily 3 are very Rockman/Mega Man PSX feeling.
Rockman No Constancy is renowned as one of the most advanced and difficult Mega Man 2 ROM hacks. It's particularly praised for its music, which is all remixes of other games, not all from Mega Man games: