A Hind D gunship at the top of tower in the middle of a blizzard in the middle of a pitch black night. The power of the boss coupled with the mood of the environment makes it quite iconic.
Later you fight Sniper Wolf in a Sniper Duel. At night. In the middle of a blizzard.
The battle with Vulcan Raven in the freezer room. It's Bomberman on crack.
Snake vs. REX. You've just witnessed the seemingly immortal Grey Fox get killed, you've watched the absolute Tear Jerker of a sequence where Snake can't bear to fire his Stinger missiles at Fox, and after it all, you just want to Kick. Some. Ass.
This is taken up to eleven in the Gamecube remake Twin Snakes. Gray Fox pulls off his Dying Moment of Awesome with even greater style. Dodging machine-gun fire, blocking it with his katana before hurling it straight at REX's radome, charging the monster head-on (losing pieces of his Cool Mask in the process) and, for the sequence when he finally blows up the Radome, his cannon charging to life with a hesitant-but-rising frequency that embodies the wounded Gray Fox gathering all his resolve for one last volley. And finally, when he's dead, Snake picks up his katana, gazes along its blade as if remembering the whole of his friendship with Fox...and then whipping the sword around and slamming it into the ground like a gravestone before charging REX head-on.
There's also the battle against Liquid Snake. It starts out as a timed fist-fight, and then later on you have to shoot Liquid while on a Jeep with Meryl (or Otacon, if Meryl died), as he follows on another Jeep while escaping Shadow Moses.
In Metal Gear Solid 2: Sons of Liberty, you fight a Harrier — in other words, a fighter jet — piloted by Vamp and Solidus. Accompanying you in this battle are Snake and Otacon in a helicopter, making for an awesome 3 vs. 2 battle.
There's something about RAY, 'cause the fight against the RAY army is sufficiently great. You play as Raiden on foot with a Stinger launcher, fighting anywhere from three to twenty Metal Gear RAYs. All the while dodging bullets, homing missiles, and water-jets. It's one of the more difficult fights, but so satisfying.
The sword fight with Solidus at the end of the game is also pretty good.
The Substance version of the game has "External Gazer", which concludes with Snake fighting Solidus...with nothing but his fists!
Metal Gear Solid 3: Snake Eater gives us The Sorrow. He's an unusual boss, because he's already dead. He's another in a long tradition of Hopeless Boss Fights- you can only win by trudging past the ghosts of everyone you've killed. He also has some of the best dialogue in the game before the fight.
The Sorrow:The living... may not hear them. Their voices... may fall upon deaf ears. But Make. No. Mistake. The dead... are NOT silent. Now you will know the sorrow of those whose lives you have ended.
Made more awesome by the ghosts. If you kill a guy with a nut-shot, he'll grasp his crotch and yell "I'm useless!" The prize for the most creative ghost goes to the one where you kill a sentry on a mountain, let a bird eat him, kill the bird, and eat it, the ghost appears with the bird on his shoulder crying "You ate me!"
The End stands out. The End is a sniper around 100 years old, and is more or less capable of manipulating the natural environment. This, combined with the fact that he is the only boss to never kill Snake, makes him a tough but somewhat forgiving challenge. You can literally spend hours crawling on your stomach scanning the combat area, that spreads over three large open maps, with your gadgets to pinpoint his position before getting shot and he runs away to a new hiding spot.
The End has some extremely crafty AI, too. You can use the Directional Microphone to learn that he's hiding in the next map, by listening for his breathing. Then, when you enter the next area, you find that he was waiting for you right in the transitional area, and he smacks you down with a flash-bang. Or you find his sniping point, but can't reach it from the same map. So you go to the next area, re-enter from a point where you can reach his perch, and find that he isn't there anymore. Instead, he's at a completely different perch, and has his scope trained on his old spot, so even if you have 100% camo, he can still completely sucker you.
The battle with The Fury inside the tunnel in the mountain. The atmosphere during this fight really adds to it, as does the music.
Fighting against The Boss was the highlight of the game. You are both standing in an open field of white flowers, with the boss not only being blond and pale skinned, but also wearing her iconic white combat suit. Being able to CQC her like she did Snake was amazing. She tells you you have 10 minutes to kill her before bombers will blast the whole place to ash and about 5 minutes into the fight, an instrumental version of the theme song, which you have heard several times during the game, starts playing. And it is clear that when the last note plays, it's all over. Unfortunately, the game makes you pull the trigger on the Boss to finish her off.
The Metal Gear RAY battle. Bonus points for quite possibly being the only time in the entire series where you get to pilot one of the titular Metal Gears.
Even more awesome when you know you are fighting the Metal Gear DESIGNED to obliterate Metal Gear REX, AKA the very one you almost destroyed in the first game and you are piloting now.
Another candidate for the greatest boss battle in the entire series must be the final battle between Snake and Liquid Ocelot. It's not very unusual or spectacular, but uses the health bars and theme music from all four games, to take you one more time through the entire series before it finally comes to an end.
Laughing Octopus has perfect camouflage abilities and you fight her inside a small hut, where she can hide in any place and disguise herself as anything, becoming part of the walls or the furniture, but always leaving some tiny traces by which you can spot her if you look carefully enough.
Although MGS4 is a single player game, when Raiden comes to Snake's rescue when he has to fight both Vamp and the Gekkos, the game gets into split screen mode to show both fights next to each other. While you don't have any time to watch what's happening on Raiden's side, it's still an amazing effect and really feels like Back-to-Back Badasses.
The second battle against Peace Walker/Basilisk in Metal Gear Solid: Peace Walker is extremely intense and very much awesome, even though it can be a long-haul on single player. The exhilaration and intensity peaks when it readies its nuke for launch, which will end in a game over if you don't stop it, accompanied by Kaz sounding genuinely panicked as he urges you to prevent the launch via your radio. Few moments are as pulse poundingly exhilarating to a gamer as that moment where the timer reached the single digits, and on their last shot they manage to stop the launch sequence for another few precious moments.. The subsequent internal destruction of The Boss AI pod as you constantly hear her voice talking to you counts as well.
Also from Peace Walker, we have the final battle against Paz and Metal Gear ZEKE. The fact that Nana Mizuki's Koi no Youkushi-ryoku is playing in the background turns the fight against a Metal Gear, something that is already awesome in its own right, in a heated, epic showdown you know you Simply. Cannot. Lose.
The first boss, Metal Gear RAY. It's constantly firing missiles at you (which can be destroyed before they explode). Instead of its high-pressure water cannon from MGS2, it has a Plasma Cannon. Parrying its attacks and damaging its feet allows you to slice off its armor, and the first part of the battle ends with Raiden slicing off its right blade. The second part of the battle is mostly the same, but in a more confined area with Raiden elevated to RAY's face. You can slice off its head armor and guns, then it launches a salvo of missiles at you which Raiden proceeds to jump across so that he can slice off RAY's remaining blade. Even after that, it's not over, as now, you have to run down the side of a building, avoiding gunfire, missiles, and the Plasma Cannon, so that Raiden can stab his blade through the head of RAY and slice it in half length-wise!And this is only the first boss!
Although relatively casual due to the Dwarf Gekkos' nanopaste, Mistral offers an entertaining fight as the first Winds of Destruction. As the fight continues, the two fighters start moving to other areas, and end duking it out surrounded by fire.
Monsoon, who definitely tests your knowledge of parrying. Set amidst a rainstorm, in a one on one duel, he leaps back and forth, giving you only a moment to react. He spends half the fight being entirely immune to your attacks by simply breaking apart around your swings, meaning you have to figure out how to get past that obstacle. He throws massive pieces of debris that you slice to pieces before they hit you. You really need to know the game by then, and when you do parry his various attacks, you really do feel like a badass for being able to get through all his defenses. He also gets one of the most metal songs for a theme song, really driving up the adrenaline. If you were brutal against Monsoon, he literally begs you to stop attacking.
Jetstream Sam, this time being a rematch with your arch nemesis. A sword on sword duel with no complications. Just you and your reaction time against a powerful cyborg swordsman with several fast attacks, and again, a really metal soundtrack.
You thought the Metal Gear RAY battle was awesome? Just wait until you go toe-to-toe with Metal Gear Excelsus, a Humongous Mecha the size of a city block, armed with massive HF Blades and plasma cannons! After slicing off its front legs, Raiden proceeds to throw the boss over his shoulder, rips off one of its blade (which are as long as Metal Gear RAY was tall), then uses that blade to parry Excelsus' other blade before cutting it to pieces! And the boss' theme...
Steven Armstrong, a multi stage boss where you spend several sequences helplessly wailing away without being able to cause any damage before Bladewolf throws you Sam's sword, evening the fight. Meanwhile, the boss throws huge pieces of debris while you only have a moment to precisely slice in two, rewarding you with slamming your blade in the boss' face and sending him flying into a wall. You also get to be involved in a punch out that ends in an epic right hook around the boss' arm. Finally, in the most appropriate way to end the fight You perform multiple precise Blade Mode slashes on the armor around his heart before you perform the same move you've been doing all throughout the game and tear out his heart.To top it all off, his theme is one of the finest boss themes in gaming.
From the Bladewolf DLC, we have Khamsin, a crazy American ex-soldier in a mech suit with a rocket powered chainsawaxe. He has a lot of cool-looking attacks, he can move faster then you'd think given his size, there's a stealth section, and his finisher (cutting apart his mech, ripping him out and carving him up in mid-air) is satisying to do and awesome to watch. To top it off, his boss theme is the previously unused but blood-pumping "Hot Wind Blowing".
While most of the fights aren't as spectacular as the rest of the franchise, special mention has to go to the obligatory battle with the Metal Gear of this franchise, Metal Gear Gander. This boss fight is split up into two stages, and each stage is relatively awesome.
The first stage has Snake running beneath Gander as it lumbers towards you. Gander will try to step on you, or will burn you with its built in flamethrower should you get too close. Becauase it has one. The only way to stop Gander is to either plant C4 where it will step down, or use land mines. Eventually, Gander will crumble from the proverbial hotfoot...
...but it's not over yet. Now you have to deal with the defenses on the top of Gander. Snake has to dodge auto-fire turrets, spread-shot turrets, anti-air missile launchers (that somehow work inside a confined freight elevator), and even aerial drones. Oh, and the flamethrower isn't out of commission either, so the fight ends with Snake chucking grenades into the mouth of a flamethrower that is currently turning the battlefield into nothing but flaming rubble.
Viper himself will spam Flashbang grenades in a deperate attempt to run down the clock - which means it becomes a demented game of hide and seek with the world on the line... unless Viper decides to hit you with his shockwave attack as you see him, throwing you across the room.