He's blue, he's fast, and he's met lots of awesome bosses over the years.
Metal Sonic in Sonic the Hedgehog CD. Rather than being a conventional boss battle, you're required to race him through the stage, maneuvering past obstacles on the course and his attacks against you.
The Death Egg Robot from Sonic the Hedgehog 2. This was where Robotnik showed just how difficult he could really be, despite the fact that you've spent the last seven or so levels kicking his ass.
More so when fighting him for the first time and finding that unlike every single previous boss in both games, he doesn't go down in 8 hits, but in 12.
You also get no rings, meaning you die in one hit. The final zone is simply two boss fights, the first of which is a Breather Boss in the form of an early version of Metal Sonic. Even as a Breather Boss, he and the following fight against Robotnik are extremely harrowing since, prior to this, you could survive indefinitely on a single ring if you knew how, but now there is no room for error.
The epic aerial battle at the end of Marble Garden Zone in Sonic the Hedgehog 3 deserves a mention here. If nothing else, it's an excellent display of teamwork between Sonic and Tails.
The Act 2 boss for Flying Battery looks, at first, like the boss of Wing Fortress Zone back in Sonic the Hedgehog 2, only you can't fight back, the area is closing in, and the mini-boss music is playing. After some time, the ship takes enough damage from the laser that Robotnik's console blows up in his face. Now Sonic (or whoever) runs after him, getting caught up in the destruction (which isn't as bad as Marble Garden until you realize you're thousands of yards in the air) and getting carried by the barrier up past the top of the ship. Then Robotnik grips onto the girder you're on and the real boss music starts up. It's easy, but it really sets the mood for the kind of bosses you'll be fighting in S&K.
Great Eggman Robo of Sonic & Knuckles. After beating the normal level boss, Sonic chases Robotnik onto a platform where he promptly gets in a giant robot that is actually bigger than the screen. After the hands are destroyed, it starts breathing fire and firing a laser that takes up half the screen at you. After it is defeated again, Robotnik starts trying to escape with the Master Emerald and you have to chase after and defeat him while the entire space station is falling apart. But it doesn't even end here, folks. If you have a full set of emeraldsnote either set will work, he pulls another giant robot out of nowhere and flies off into space, while Sonic transforms into Super/Hyper Sonic and chases him through a asteroid field, all while having to dodge laser blasts and constant Macross Missile Massacres. Perhaps the single greatest Moment Of Awesome in the entire series, and especially satisfying if you have played through both Sonic 3 and Sonic & Knuckles to get there.
Big Arm from Sonic the Hedgehog 3. This is the one time Eggman did what he otherwise could never do: defeat Super Sonic. Sonic goes into Super Mode, tries getting a cheap shot in, gets grabbed, and Wham! The Robo-Suplex knocks every last ring out of you and smacks you back into normal form. This, of course, is if you hit below his microscopic hit box...hit above it, and say hello to the spikes. Which, at this point, will now be a horrendous threat to you. (Especially if the recoil of hitting them knocks you into his Eggbot's hands...)
The boss fight at the end of Knuckles' story in Sonic 3 & Knuckles. After you defeat Mecha Sonic as Knuckles the first time, he seems like he's down and out, but then he uses the Master Emerald to go into a Super form, the first time in the series a Sonic robot goes into a Super form. Check it out here.
Egg Viper from Sonic Adventure. Simple Sonic vs. Robotnik battle, nice and challenging, plus that final move he pulls on you after you deplete all his health is quite unexpected when you first fight it.
Perfect Chaos from Sonic Adventure was a gleefully epic way to end the game - Super Sonic in 3D for the very first time and everything!
Also from Sonic Adventure, Beta Mk. 2. A truly epic final battle for Gamma as she fights with the first of the E series. The MUSIC alone just makes the battle awesome, coupled with the setting, the flow, and how the battle plays out. Despite technically being unable to do anything until he leaves himself open, you get an epic feeling as you exchange shots with each other in an attempt to gain the upper hand. And even when you win, Beta still does better than most Sonic bosses by getting in one last badass hit.
Sonic Adventure 2's Biolizard. The Prototype Ultimate Life Form versus the Real Ultimate Life Form, in an epic battle. The fact that its weak spot is so hard to reach is what makes it awesome — and those lightning balls! And the final hit, where you're stuck floating helplessly through the field of bubbles, and just have to hope you have some rings left over! And the sounds! The music is awesome, with really deep lyrics — but good luck hearing the lyrics, or even the music most of the time, over the roars of the boss and the sound effects of its attacks. Absolutely awesome.
Sonic's battle with the Egg Golem was pretty epic, too. The cutscene in Dark Mode basically compressed a battle that originally took about 3 minutes after you'd mastered it, and due to the fact that while hitting it is hard, not getting killed is easy, could easily take you twenty minutes on your first try, into a few seconds — a great injustice. Egg Golem is awesome. Then again, the broken Egg Golem that Eggman has to face in Dark Mode is a pushover, so they had to make Sonic seem that much more awesome to keep him from being overshadowed by Eggman in Egg Golem-smashing prowess.
The Final Hazard. One, requisite Super Sonic fight, only this time, also with Super Shadow. Two, the epic music, "Live and Learn" by Crush40. Three, the fact that the Super flying physics blends the much-hated Knuckles/Rouge swimming and gliding physics faithfully but gracefully, making all that Unexpected Gameplay Changing worthwhile. Four, the most gorgeous renderings of the characters involved in the whole game. Five, commentary from every single playable character (and one not) that, in the case of Eggman, contributes heavily to his characterization. Six, the heart-wrenching dialog between Sonic and Shadow as Shadow begins to weaken. Did we mention "Live and Learn?" Yeah, we did.Devil Doom in Shadow the Hedgehog is epic for almost exactly the same reasons, particularly Three through Five/Six.
It's also epic in the respect that Sonic and Shadow finally team up with one another, knowing what they must do to save the world. The transformation sequence alone is enough to make your blood pump.
The second and final hedgehog battle. High speed battle with eerie lighting and dark music. Epic incarnate.
The Duel Boss between Sonic and Blaze in the first Sonic Rush. Fighting something so similar to yourself is always fun, and once you deplete the boss to 1 point of health, the two combatants charge up their powers and clash into each other head on; either you get the kill, or lose instantly, it's intense. Yes, the final point turns into a test of button-mashing speed, but it is such an epic button smash.
Almost every boss in Sonic Rush Adventure has some really weird and awesome fighting styles or weak points. Honourable mentions go to Machine Labyrinth, where you smack balls up to hit this monkey like thing at the top, and there's three which all do differing amounts of damage (different sizes) and take different levels of momentum to hit, Haunted Ship, with a fight with a giant robotic pirate with its weak point being a gem that flies around, and Blizzard Peaks, where you go inside a robotic whale and do an obstacle course to the weak point to inflict major carnage. Oh, and Coral Cave, which while it is fairly standard, when it turns red before it smacks you underwater, it makes a STEAM TRAIN NOISE. Still a fun fight overall though. Even the FIRST BOSS is a giant mecha T-rex, and while it's piss easy, it feels so epic.
Alf Layla wa-Layla from Sonic and the Secret Rings. Nice departure from the regular final Sonic bosses (no Super Sonic and you CAN get hurt in this boss fight). Challenging as heck and, for the first time in a game, Sonic actually pummels the living daylights out of a boss.
Alf Layla wa-Layla was fun to beat the hell out of, but what about BEFORE he's Alf Layla? Fighting Erazor Djinn is fucking awesome. For one, "It Has Come to This" is the perfect song to describe the fight, two, you have to run with him as he slashes with his giant razor, three, you have to SPEED UP during your quickdraw stand off just to hit him!
Not to mention that Sonic defeats the Egg Dragoon by removing the Egg Mobile from the rest of the machine. Sonic learned how to make the most out of his newfound strength pretty quick.
The final bosses of Sonic Unleashed. It's Sonic and Chip who is actually the Light Gaia/Gaia Colossus! vs. the monster that is Dark Gaia. It's half Punch-Out-styled fight, half dash-to Gaia's weakpoints-and-destroy-them-For Massive Damage. It all culminates to a Super Sonic (complete with NiGHTS-esque gameplay!) and the Gaia Colossus vs. the Perfect form of Dark Gaia.
When Chip's chasing ancient evil in a frigging BUILDING and slugging twenty-thousand tons of antiquated stone into its face, you know it's hitting the fan. The sheer determination on Chip's part (Pushing through the shield separating him and Dark Gaia comes to mind) completely flabbergasts Super Sonic. The awesomeness is only amplified when Super Sonic comes into play, drills the six arms holding Chip and the Gaia Colossus in a crush, and proceeds to Needle Drive Perfect Gaia's eye. With his own body.
In the last phase, you Super Dash Dark Gaia through the eyes.
Metal Madness/Metal Overlord, the final boss of Sonic Heroes. All four teams end up having to fight him at some point, and each portion is harder than the last. The final part, of course, is as Super Sonic/Tails/Knuckles.
The music makes the final part feel so much more epic as well, and the fact everyone eggs you on, and the altered team blast, and the fact that Metal Overlord throws parts of the EGG FLEET at you!
Egg Albatross is pretty amazing, too, considering that you're really only about halfway through when you get to it. It's set up as though it's something more, though, with the cutscene afterwards advancing the plot considerably. A perfect way to end the first half of the story mode.
Really, though all three Eggman fights have their flaws, they still effectively present the fact that in this game, he was going all-out on Sonic and his friends. You have backup in the form of your two allies and their team-based attacks; Eggman has multiple gunners riding tandem with him in his much larger vehicles, and on-foot escort units, all of whom are looking to smear all three of you onto the floor!
Robot Carnival but especially Robot Storm. Just fighting loads of robots, but mass carnage is to be had.
The bosses from Sonic and the Black Knight. Sure, most of the bosses are easy (once you figure out the quick way to kill them) but both King Arthur fights were cool with you having to race his horse, jump up and cut the mess out of him. Plus, the battle theme is called "Fight the Knight".
Then, there's the REAL final boss Big Bad, The Dark Queen. Seriously, you transform into Excalibur Sonic, complete with a holy BFS. Plus, with the creepy With Me playing in the background, this fight is just...awesome. You and the boss are just floating in the middle of nowhere, and you have to block her sword swings from ALL FOUR of her arms. Then, with the way you finish her off in the end? That's literally an epic win.
And finally, the bonus mission where they decide to turn Lancelot into Shadow the Hedgehog with armor and a sword. If you thought the first Lancelot was easy, this one is here to make up for that.
Egg Pinball in Sonic Advance 3. You hit Eggman underneath a platform by hitting these balls to turn them red, and they bounce around the room. Gets completely mental towards the end as the music and the speed of the attacks increases.
The Nonaggression boss also counts; after defeating the final boss, Gemerl goes haywire and uses Chaos Emerald to transform into Ultimate Gemerl, and Sonic turns Super to stop it. It's a lot like the finale of Sonic & Knuckles, except you have to team up with Eggman to bring it down. Of course, this boils down to using Eggman as the focus of a Kamehame Hadoken and then ramming the boss' weak point with a Super Sonic tackle attack. Halfway through the fight, the boss goes even more haywire and starts spinning wildly, challening the player to stay between its flailing mecha-tentacles.
It's difficult to have something visually spectacular on the Game Gear, but the Marveshupopolous-gou in Sonic The Hedgehog Triple Trouble's Sunset Park pulled this off. Sonic is zooming along the top of a long train as Badniks and spike balls are flying at him, with only the 5 Rings provided to him at the start. As Sonic gets close to the engine at the front, he'll encounter gaps he must jump over lest he gets smacked by a thousand tons of steel. On top of that, this boss battle has a unique theme. This train is long enough to constitute its own Act.
Sonic Colors has the Egg-Nega Wisp, especially on Wii. Let's summarize; Egghead is on his last legs. The entire floating amusement park you've spent the game on is blowing up, very fast. And now you're running through the aptly-named Terminal Velocity towards the planet, while Eggman pulls out his final weapon. After facing off with nothing but robots, you finally get to take Eggman on in head-to-head combat, battling evil versions of the Wisp powers you've been using. All while some of the most epic music in the game is blaring in the background. And the best part? Halfway through the fight, an orchestrated version of Reach For The Starskicks in,and it is kick-ass. And you finish it off with the pure awesomeness of the Final Colour Blaster. Sonic didn't just [finally] break through the Polygon Ceiling with this boss; he shattered it.
The completely changed Silver boss fight in Sonic Generations. To start off, there's already a great remix of "Vs Character" from Sonic the Hedgehog (2006) playing in the background. Second, instead of Silver grabbing you with his psychic powers, yelling "IT'S NO USE!" and then launching you with a "TAAAKE THIS!" to your soon to be caused-by-glitch death, he's chasing you through Crisis City launching stuff at you. Third, the way you attack him is just SO awesome! You homing attack on multiple platforms and then hit him and he crashes to the ground. Or, you're running on a car crafted from other cars, and homing attack him! Fourth, the end, when he only needs one last hit to take him down. Silver crafts a gigantic ball of junk, with a yell of "METEOR SMASH!" as said giant ball of junk rushes at you. Just to make things more tense, he's also thrown in a container to attempt to crush you with just for a back up plan. With two things trying to smash you at once, and both are dangerously close to you, what does Sonic do? HE DODGES THE CONTAINER, AND HOMING ATTACKS SILVER, WATCHING AS HE GETS CRUSHED BY HIS GIANT JUNK METEORITE. It's just a really fun, exciting, and fast paced boss fight that tries to do 2006 and Silver some justice.
The handheld version doesn't lack good bosses either. Returning from Sonic Adventure 2, we have the Biolizard, only fought as Sonic this time, and with controls adjusted to a 2D plane just like the bosses in Sonic Rush. Does it work? Oh hell yeah, yes, it does.
On the subject of Adventure-era bosses in Generations, there's Perfect Chaos in the console/PC version. It really shows how far Sonic's come. In the original Sonic Adventure, Perfect Chaos was the True Final Boss, fought as Super Sonic. In Generations, he's just the second boss (discounting rival battles, he's likely to be the fourth fought if you count the rival battles as boss battles) of four. How do you deal with the water problem (you don't get Super form in the Generations version of the battle)? You boost across it! Upon the final hit you have to do platforming to land a homing attack directly on the weak spot.
The 3DS version's Egg Emperor battle is the perfect example of how to take an awful boss and fix it. The boss fight is conceptually similar, but considerably streamlined: he no longer spends half his time blocking your every attack with his shield, he takes the standard eight hits rather than having massive HP to gradually chip away, and most of the distractions are gone. Essentially, it's everything the fight should have been in Heroes.
The console version's Time Eater is often slammed for being a very bland final boss. However, this is not true of the 3DS version's Time Eater. Both Classic and Modern Sonic have unique parts of the boss fight. Classic has you just a short distance away from the Time Eater, dodging his attacks, which get more and more varied as the fight goes on, as well as harder to dodge. Modern Sonic has you boosting towards the Time Eater, all the while trying to avoid its force field attacks and trying to fly through rings of rings in order to replenish time, and his attacks also get more varied and harder to dodge as the fight goes on. His Warping Arm attacks now require you to boost out of the way or get a guaranteed hit, instead of just flying past it, then Eggman unleashes several clocks whose hands you have to dodge. Finally, instead of simply holding two buttons down, the final blow involves dodging Eggman's last ditch attacks, then ramming into him.
The final battle of Hero/Dark Story mode in Sonic Adventure 2 deserves a mention too. It ends up being a bit of an annoying Puzzle Boss but the buildup is brilliant, making this the final battle of each story between rivals Sonic and Shadow, with the fate of the world at stake. The awesome music helps too.
Sonic Generations recreated the battle, adding an intro mirroring the SA2 intro sequence and a short burst of "All Hail Shadow" if Shadow sets off his super move.
The final boss of Lost World gets points for style, some polarizing attack patterns aside. Eggman created a mech powered by the energy of the world, with a cape made of said energy. It's like the Death Egg Robot as designed by Go Nagai.