Mega Man 1 brings us the Yellow Devil. So you've taken down the original six Robot Masters and have finally started the assault on Dr. Wily. At first nothing really out of the ordinary, just retreads of enemies fought throughout the game. Then you enter a boss room only to find no-one waiting patiently. Suddenly, from the LEFT SIDE of the screen comes a barrage of yellow orbs, leaving you scrambling and dodging, wondering where it's going to come next, and as each orb reaches the right side, it starts forming into something much bigger. Finally, the Yellow Devil takes full form just long enough to fire ONE bullet right at Mega Man at high velocity, and you barely have enough time to dodge before you have to worry about the creature deforming and again sending its orbs across the screen. This continues, leaving you with only scant enough time to hit its weak spot... the very same eye it uses to fire at you, and even when you know the pattern of its reformation, it's still an exercise in thumb athletics to get through this battle with minimum damage. Truly a helluva way to introduce the different bosses of the Wily stages. For extra epic, take it on with just the Mega Buster, and add required precision to do damage.
Mega Man 2, on the good ol' gray box. The Dr. Wily boss fights (especially the Mecha Dragon and Guts-Dozer) were JAWDROPPING by 1988 standards.
The fight with the Wily Machine is fun, if easy. The preceding Robot Master Boss Rush also deserves a mention.
Another example would be the two Bass battles that you have to win in Mega Man 7 as long as you don't use the Super Adapter for those fights. In the first one, you go face-to-face with Bass who has the all the same basic attacks you do. When you face him for round two, Bass uses the equipment he stole from Dr. Light to fly around the room, that happens to have lowered gravity. In both fights, you have to stay on your toes as long as you don't use the aforementioned gamebreaker or healing items. Sadly, he becomes a total push over in Mega Man 8, despite him supposedly becoming a more "powerful" form for that battle.
Alternatively, you can hold back against Bass in the first fight, maybe using his weakness weapon (Crush Noise) if you're having trouble, and when he breaks out his Super Treble Adapter, that's when you break out the Super Rush Adapter. Then it becomes an epic, evenly matched midair duel, with both of you zooming around on jet packs, firing buster shots and homing Rocket Punches at each other as you pass by. It's still a challenging fight because the combatants are dishing out heavy damage with each shot, and Bass is stronger and more maneuverable then Mega Man, with infinite flight as opposed to Mega Man's glorified Double Jump. It makes the weakened Treble Adapter in Mega Man and Bass all the more painful to see...
Mega Man 9 gives us the final Wily fight. It's a three-stage fight with no breaks in between. It's also very hard, but the feeling of satisfaction you get from beating it is awesome.
The Weapons Archive boss in Mega Man 10. It's separated into three parts throughout the level. Why? Because the fights consist of 9 machines, each taking its attack pattern from a robot master from a previous game. Elec Man from 1, Wood Man from 2, Gemini Man from 3, Ring Man from 4, Napalm Man from 5, Flame Man from 6, Slash Man from 7 (with an appropriate 8-bit sprite to boot), Frost Man from 8 (also packing a new 8-bit sprite), and Tornado Man from 9. If that isn't an excellent callback to the Classic series as a whole, then nothing is.
One of the bosses in the franchise that stands out is X1's Sigma. For once, a main villain actually faces you man to man... not piloting a machine, as Wily does, but facing you head on!
Try doing that fight with just the X-Buster. You now need to fully charge the buster, and it will only deal a single point of damage to him! Not only does Sigma become insanely hard but the sheer length of the battle makes the eventual win very satisfying.
Megaman X2's Zero fight. Although you can easily dodge most of the attacks, the music makes up for it.
Sigma in X4. Although Sigma is usually a great boss, Mega Man X4's rendition was just über-cool. Grim reaper, then the agile saber/electric version, but the top of it is the final form. A giant head AND a giant robot teleporting in an out while some elemental robot heads help them. You'll need to be really good at pattern catching to beat each of the variations of the third Sigma form.
Sigma's final form in X7. Say what you will about X7, but the final battle with Sigma made everything worth it. Sigma is fought in his biggest body ever, in what appears to be some sort of odd void (despite having been in a regular building earlier) with your only footing being small floating platforms. As the fight begins, Sigma rises up and says in the most hammy voice ever: "Ready for the real thing?!" Then he proceeds to attack in you in a remarkable number of ways, while a truly epic song plays in the background.
Despite having followed the abysmal Mega Man X7, X8 was a good game with some sweet bosses. The highlight was undoubtedly the return of Vile, with his new green armor apparently signifying how much more maneuverable he is than in previous X games. Then you get to Lumine using all the screen-filling "anger" attacks of the eight main bosses...
Not to mention his final form. Lumine gets into the shape of something that is almost angelic, while throwing very special attacks at you. But that's not all. Eventually, Lumine goes Ax-Crazy and starts BSODING just teleporting doing nothing. If you let him live long enough, he will reach a moment in which he says "I won't let you go, NOT YOU!!", the screen goes black and you die.
Mega Man Zero gave us the Copy-X fight. Fighting against what was basically the main character previously is pretty cool in its own right, but when he finally goes One-Winged Angel on your ass... The music alone makes this fight epic.
Mega Man Zero 3 gives you the three-stage battle against Omega. While the first bit is something of a yawner, consisting of the very first boss with a palette upgrade and some extra attacks, the second form is significantly harder and more awesome, putting you on a falling platform faced off against a boss made of gargantuan, warped versions of X and Zero's heads... and then you get to the final stage. Landing in the very first room from the first Mega Man Zero, now engulfed in a sea of flames, and facing off against Omega's core: theORIGINALZero, who is faster and stronger than you and has some of Zero's most broken moves from the Mega Man X series. All this while "Cannon Ball" is blaring at you.
Also from 3, we have a hidden Bonus Boss in Sub Arcadia (the stage before the final level): Phantom, who died two games prior when he sacrificed himself to try stopping Zero. This battle takes the original and turns it Up to Eleven. His attacks are deadlier and harder to dodge, he can make false clones of himself, and if you attempt to bum-rush him you WILL have your metal rear end handed to you. Phantom also has just as much health as each of Omega's forms, and once you deplete them, you feel fantastic, having bested a foe that is in a one-screen-large room which offers minimal room to dodge and is far faster than you.
The fourth game's Dragon, Craft is a tough Wake Up Call Boss when you first meet him and find he has three life bars rather than the usual two. It's a tough close range battle where you can smack his projectiles out of the air and a lot of fun.
Finally there's the final battle of the series againts Dr. Weil. First, he fuses with Ragnarok's core and uses a variety of cool attacks, including summoning the souls of the last game's bosses to fight you. After that, he goes One-Winged Angel. Cue an epic battle on top of a flaming space station hurtling towards earth while kickass music plays in the background, and you have a badass last hurrah for a badass hero. Now that is how you do a Grand Finale.
Made more satisfying by the fact that you've been waiting since Zero 3 to get your hands on the bastard, after all that he has done. And having the Badass deal the appropriate justice (oh, the irony!), well, nothing more needs to be said...
Wait, there's more; This battle is not just awesome, but meaningful — Zero finally finds his resolve and a reason to fight in this war, something that bugs him for centuries (since X4, to be precise). And he also states that he isn't a hero and he will do anything it takes to fight for those he believes in. Not to mention him finally ending the centuries-long war and creating peace between humans and reploids, something that Dr. Light aims for with Zero's best friend X (who dies in the end of Zero 3), and the awesome irony behind it: he was created by Dr. Wily, Light's nemesis, to destroy X and later wreak chaos in the world. In short, Wily's creation ended up fulfilling his nemesis Light's dream.
Really. The best part of that battle can be summed up in 4 little words: It's Zero's last battle. Because of that little fact, you know that they have to make it awesome.
It's even more epic if you picked up the axe weapon from an enemy, and use it for the final blow.
Omega's first two forms would've been even more epic were it not for the GBA's hardware limitations.
The Omega fight also has immense symbolic value. The fact that Zero's essentially fighting the very thing Dr. Wily INTENDED him to be. It's the ultimate way to give fate the metaphorical bird. Also, Omega is symbolic of the inner demons that have been tormenting him since the X series. Zero is essentially gaining some well deserved closure.
The Bass battles from Mega Man Battle Network 6 were all pure adrenaline. The first one, if taken onearly enough, is usually the player using their first gained Cross's charge shot to constantly interrupt his Buster Rake at just the right time. The SP battle is simply the first one with a 900 HP bonus and a little faster. However, it's his BX form that really shines. First off, you have to defeat your Beasted-Out Evil Twin, which is an absolute joke, and you will probably be able to beat it in your sleep, due to him kicking your ass so many times. He's literally faster than Quickman, has a Buster Rake that literally cannot be dodged without ice panels or a seriously crippling glitch, has all his former attacks which now deal enough damage to make Mega Man go angry in a single hit, and his ultimate attack, pulling out your opposite version Cybeast's severed head and using it to spit out its signature attack, which does well over six hundred damage. Oh, and he has over 3000 HP, and drops one of the most disappointing Giga Chips of all time. Still, he's pure adrenaline every single battle.
Fighting the LifeVirus, a 1000 HP monster with a 100 HP shield, and a constant spawn of drones, is probably the most fun part of the original Battle Network.
The Omega/Original Zero battle in Mega Man ZX. There is just something about fighting something that just seems to do anything you can do, only looking more badass at it (see for example his EX-Skills). Complete with Cannon Ball "Hard Revenge" and the increased Berserker-ness of Omega.
Also the Prometheus and Pandora fights in both games, which never cease to be entertaining. Their boss themes help a lot.
One of the most fun bosses in Mega Man ZX Advent is the fight with Atlas. At that point in the game, half of the forms cannot be used (Chronoforce and Rospark). And unlike the other bosses, she does not do anything to go off of the screen like the other bosses. She does, however, wall jump, which the others do not do. So in this fight, both fighters stay on screen at all times, wall kicking, shooting, and dodging. It feels like you are playing against someone else who has the skills that you do.
The other biometal users in Advent also count, especially Vent/Aile. It's an easy fight but the cool cutscene beforehand makes it feel epic.
These fights are doubly fun in Boss Select mode when you can take their form and beat them at their own game.
The Final Bosses from both games are epic struggles:
From the first game, the final boss' first phase fights like a Street Fighter game complete with a freaking Shoryuken move! Then in round two the boss goes through three stages in one form, continuously changing the method needed to attack it and upgrading its own attacks mid battle.
In the second game, the ultimate battle starts out with a three headed dragon in the first phase of the fight. Then in the second phase the boss uses upgraded attacks from all the other Mega Men including yourself. Oh, and the final battleground is made out of the Bigger Bad in a room designed to look like a broken paradise. Now that is awesome!
Crimson Dragon is notable for being a unique boss fight, and for the wholetimeline, at that. It is the ONE boss fight where you fight the Big Bad directly, not just his monster.
Also from Star Force 3, Sirius. His fights involve lots of dodging and waiting for the perfect moment to strike, keeping you constantly alert. When you finally get in some good hits, he doesn't even flinch. Winning his fight is hard, but it gives such a sense of satisfaction.
Also, Rogue at his highest levels. Bringing him down is one of the most rewarding moments in the whole series.
The battle with the Gemeinschaft. All of the pirates, except Bola and Klaymoor, who ditched at the last second, make one last attempt to take you down. Roll fixes up another train car and you chase them while you are on the roof of your train, hitting their cannons, Birdbots, and Servbots. The music's pretty cool too.