Nightmare in Metroid Fusion, who was foreshadowed throughout most of the game. Other M retroactively makes it even more of a Climax Boss, as it's revealed Samus encountered it before.
Pretty much any major boss in Super or the Prime games except for the last two or three on account of being fought so late.
The battle with Frenzied Toroko in Cave Story mixes this with a heaping helping of Player Punch for even more of a dramatic effect.
And then there's the Core fight, which comes after a minor plot revelation and is followed by a more important one. Plus, it's got its own BGM track, loads of creepy atmospheric build-up, and is followed by both a Player Punch and a fork in the road.
Helmaroc King in The Legend of Zelda: The Wind Waker. It being the kidnapper of Link's sister, Aryll, as well as having kidnapped other girls and overall terrorizing the Great Sea. But it's only Ganon's seccond-in-command.
Yuga is this in The Legend of Zelda: A Link Between Worlds, appearing in Hyrule Castle as a boss with a very similar backstory and battle to Agahnim in A Link to the Past. It's after he's defeated that Link actually learns about Lorule and the captured sages.
The "White Assassin" in Mirror's Edge is actually the only actual boss fight in the game. The after-fight cutscene also makes it the Wham Level.
Ōkami has two Climax Bosses: Orochi and Ninetails. Both brings a new revelation: Orochi's death causes all the other bosses to be let loose upon the world, and Ninetails reveals the existence of Yami.
An action game example is the final battle with the Blood Ark in Another Century's Episode 3, at the end of the middle stage of the game. While it is a battle against the Final Boss pilot, and it has the first use of a specific boss battle theme, it is almost laughably easy, since your forces have been getting upgraded, and the villain is using the same mech he had at the beginning. The climax comes from the removal of his unusuallyobscuringmask.
Darth Vader in The Force Unleashed. In the Wii/PS2 version, the second duel with Kento Marek, aka., Galen's father may count as well.
And for the future DLC, OBI-WAN KENOBI AND LUKE SKYWALKER!
Several in Asura's Wrath. Each of them is an episode all on their own, or at least have a fight that lasts most of the episode. The fights against Wyzen, Augus, Olga's Fleet with Berserker Asura, The Final Deus Fight, and ESPECIALLY Gohma Vlitra are stand out examples.
The real kicker? If the DLC trailer for Asura's Wrath is any indication, The Golden Spider will be the ultimate example in the entire game.
Ninja Gaiden II (the original NES version) has a climax boss in Ashtar, who we initially believe is the Big Bad behind the game. Ryu defeats him about halfway through the game, but the threat posed by the Dark Sword of Chaos isn't over yet, and the true Big Bad turns out to be Jacquio, who you defeated in the very first game, and who has revived himself using the Power of Evil. The same Final Boss music is used for both major battles.
In God of War II, Lakhesis and/or Atrophos, two of the Sisters of Fate. (Clotho, the third sister, is more of a Puzzle Boss.)
Also subverted in III, where the real turning point of the game's plot (finding and freeing Pandora) isn't done with a boss fight at all, but a puzzle. Seems to be a common theme in this series. (Though some might suggest the rock scorpion would qualify as this trope.)
Unless you just jump on his chair and punch him in the face, then he's a textbook Anti-Climax Boss.
The Heretic Leader is another example, although he's only the first boss, he's the hardest of the three, at least on Legendary.
Legendary co-op turns all the boss fights into That One Boss instead. The Heretic leader becomes the easiest because if you get lucky, you can assassinate him in one hit. The Prophet of Regret is a absolute nightmare (you have to watch out for his teleporting chair. If his giant laser (one shot kill) doesn't get you, the grenade spamming grunts will. If they don't, then the elites (both dual wielding plasma pistols AND using swords) sure will. On top of that, if you are skilled/fast/lucky enough to survive all three, your partner had better damn well be too. The final boss almost seems EASY after that.
Strife has The Programmer. Most of the game to this point had been preparing to storm his castle. During his fight, you are introduced to The Sigil and spend the rest of the game collecting its components from his colleagues.
The Cyberdemon in Doom. It was even featured on the sequel's cover!
X vs. Zero in Mega Man X 5. This battle is built up by four games' worth of storyline (even included in a prophecy, or something close to one for a sci-fi series), gives genuine conflict to the characters involved, and one of their deaths brings about the end of the series (supposedly). The awesomebattle theme cements its status as one of the best battles in the X series (some say even the entire Mega Man continuity).
The Egg Viper in Sonic Adventure. To a degree, the Egg Walker too, but it's pretty easy.
E-101 Beta qualifies as well, and possibly Alpha/Zero. They even get their unique themes each and act as the final bosses to their side-stories.
The 3D Mario games have Bowser or Bowser Jr. fights throughout, unlocking new levels after each one.
While Sunshine followed a somewhat different formula, the Climax Boss was Mecha-Bowser, which is followed by the reveal of Shadow Mario's identity. It's Bowser Jr.
In a way, Ludwig von Koopa serves as one for Super Mario World: he's the fourth of the seven Koopalings and the only one whose attack pattern isn't recycled, and he guards the bridge that connects Dinosaur Land's two major continents.
Spyro: Year of the Dragon gives us Scorch, the boss of the penultimate world, Evening Lake. The cutscene before the fight gives a major plot revelation: The Sorceress is NOT a Well-Intentioned Extremist, which she reveals to Bianca. Bianca, this Not Being What She Signed Up For, finally performs her Heel-Face Turn. Anyway, the Sorceress needs a "Monster to End All Monsters" so she takes one of her minions, as she and Bianca have done twice already, but this one is unique. Unlike previous times, this minion is frightened and needs to be pushed over by his partner. Also, you don't see the boss in the cutscene this time. Then, we get to the actual fight, in which Bentley tells Spyro that the Sorceress is going to use Scorch to crush her enemies, starting with them. The fight is fairly challenging, though many cite it as easy. The reason is that the previous boss is considered by many to be one of the hardest fights in the game, and an optional mini-boss in a recent level is considered to be one of the most annoying.
Seymour Natus in Bevelle and later Yunalesca in Zanarkand in Final Fantasy X.
Atma/Ultima Weapon in Final Fantasy VI. He comes in right at the end of the The Floating Continent and has a boss theme that plays four times (his appearance being the first time, the subsequent ones against the Warring Triad) in the game.
Agatio and Karst in the sequel, which incidentally is the only boss fight you're allowed to lose.
The fights against Dragon-Maleficent and Possessed!Riku in Kingdom Hearts.
In Kingdom Hearts 3D, Sora has Xemnas, who appears to drop bombshells about the Organization's purpose and ends Sora's storyline but not the game. Riku has Xehanort's Heartless, and the teenage Xehanort. The last one is arguably more challenging than the final boss, who is fought after the villains' main plan is already stopped.
Tales of Symphonia loves these. Not only does it have a bunch of them, it likes to spring them on you in groups: three climax bosses in a row, one of whom is all but unbeatable: Remiel, Kratos, Yggdrasill; two in a row: Pronyma, Yggdrasill; two in a row: Kratos, Origin.
Thankfully with the first set, winning to boss 2 is optional (all you miss is a ton of experience) and you can't beat boss 3.
Unfortunately, battle 3 of the first set can be a case of kicking you while you're down because it occurs regardless of whether or not you win the fight before it, and if you lose the one before it, you start this fight off with only 1 HP.
From the same game, the Hopeless Boss Fight against Lavos. It's actually winnable if you're of a high enough level, but you'll have to go through the New Game+ before you get to that point. And go through New Game+several times before it ceases to be hard.
Vinsfeld Rhadamanthus, Big Bad of the first half of Wild ARMs 2, fought at the transition point between the two halves of the game. Bucks tradition by including major plot points immediately after his boss fight, rather than before.
Selvaria in Valkyria Chronicles, who stands at the top of a fortress and will rain bullets down upon any fool who's in the open long enough with a BFG. The strategy to defeat her is long and involved and can easily take several retries if you're not careful.
Selvaria again in Valkyria Chronicles III, because The Nameless is supposed to assassinate Prince Maximilian. Turns out she's the reason why nobody else tried doing this! And then things goes downhill from there, with The Nameless branded as traitors and Gusurg missing, only to turn out to have switched sides.
The Legend of Dragoon had roughly one per disc. Disc 1 had Feyrbrand and Graham and Freugal (second time), Disc 2 had Lenus (first time) and Disc 3 had the Divine Dragon. Freugal and Divine Dragon were variations in that a lengthy amount of plot was developed after defeating them that had nothing to do with the bosses themselves. In addition, the final bosses to the first three discs usually had a large plot bomb dropped on the player either before or after the fight.
In the Rise of the Zilart expansion, Kam'lanaut in the Stellar Fulcrum.
In the Chains of Promathia expansion, Tenzen on the airship. Omega and Ultima Weapons may count as well.
In the Treasures of Aht Urhgan expansion, Gessho in Talacca Cove.
Though not yet finished, the Climax Boss of the Wings of the Goddess expansion seems to be Cait Sith Ceithir. But considering the bombs they love to drop in every set of missions, the final fight of every mission set seems to be a Climax Boss.
Final Fantasy XIII continues the tradition proudly with Barthandelus, the true fal'Cie form of Primarch Galenth Dysley.
In the second, third, and fourth generations of Pokémon, the fights against the leader of the local crime syndicate typically take place immediately before battling the eighth Gym Leader and put an end to the main conflict of the story. In the third and fourth generations, the battle against the game's flagship legendary also takes place in the same scenario. The first generation mixes it up as Giovanni, the Big Bad, is the eighth Gym Leader. The fifth generation abandons this formula completely; the leader, Ghetsis, IS the Final Boss. Instead, the last Gym Leader acts as a Climax Boss, what with the coolness of the Gym and the difficulty of the fight.
The Eighth Gym Leaders in each game usually qualify, especially considering how much time you're going to have to spend Level Grinding between beating them and tackling the Elite Four. Giovanni is probably the best example from a story perspective, and Claire is probably the best example in terms of difficulty.
Pokémon Ruby, Sapphire, and Emerald have another Climax Boss: Norman, the fifth Gym Leader, and the player's father. Despite the fact that his Gym is closest to home, he refuses to fight you until you beat the other four Gym Leaders. During the entire first half of the game, growing strong enough to challenge Norman is the player's primary goal. Beating him allows the player to use the Surf TM, unlocking the right half of the Hoenn region. Surpassing your father is what really gets you noticed by various NPCs. And Norman represents a massive spike in difficulty compared to the other Gym Leaders.
Radiata Stories features a branching storyline that ultimately sees the main character on one side or the other of a war. Each side has Jack visiting the Fire Dragon's volcano approximately 3/4 of the way through the game, though; in the Human Path Jack attacks and slays the Fire Dragon, while in the Fairy Path Jack tries to prevent the Fire Dragon's death, fails, and engages in a Hopeless Boss Fight against Cross.
Dread Joker in Megaman Starforce 3, arguably. The fights against Jack Corvus and Queen Virgo inside Meteor G could also count, though they're both directly before the Final Boss.
Skies of Arcadia features quite a few. There are two Hopeless Boss Fights against Ramirez, and the fight against Galcian's fleet and Galcian himself near the end. The fights against the Gigas and the other Admirals, whether in their ships or in hand-to-hand combat could count.
AdventureQuest Worlds gives us the Lords of Chaos, who are all Climax Bosses save for Discordia (who wasn't really a Chaos Lord) and Kimberly (other than the health bars which players on all servers worked to get their health bars down to 0 during the One-Eyed Doll Live Event, although Kimberly had the ability to heal the health bar a few times). There's also quite a few non-Chaos Lord bosses that have special challenges for fighting them.
Escherion: While the Staff of Inversion is alive, Escherion does not take any damage.
Vath: If you attack Vath first, Stalagbite will stomp the whole party to death for massive damage. If you attack Stalagbite first, your damage is significantly reduced when attacking Vath.
Kitsune: He'll shapeshift into a giant Kitsune that's immune to your attacks for a while. Wait until he reverts back to normal to continue damaging him.
Wolfwing: He'll heal himself up to five times per fight, and once his HP drops below 10,000, that's where he starts going berserk.
French Horned Toadragon: Every once in a while, the toad will use an attack that petrifies as many players as it wants for at least two attacks.
Ledgermayne: Every once in a while, it will stop to charge up a powerful attack. Enter the glowing safe zones that open up when this happens to avoid damage. The safe zones will heal you when you're in them.
Tibicenas: He'll steal HP from as much players as possible up to eight times per fight. When his HP hits below 5,500 and he heals for the sixth time, that's where he goes berserk.
Ultra-Tibicenas: Same as Tibicenas, except he steals HP more often, goes berserk when his HP hits below 20,000, and, worse yet, petrifies you every once in a while.
Baron Luca: As an Expy of Dracula from Castlevania, he, at half-health, turns into his demonic bat form, just like Dracula himself, which deals a bit more damage than his first form.
Moganth, Udaroth, Cellot, Zellare , & Desoloth: Same as Ledgermayne, except the damage of their charged attacks is lower and only does about 500-700 damage, and you don't have to enter any glowing safe zones to avoid the attack.
Gruaige Baas: She'll petrify you for a few seconds with a laser attack every once in a while, plus, also every once in a while, except later, she charges powerful attacks and hits for about 500-600 damage.
Khasaanda: She can sometimes lock your skills for a few minutes when you use them, plus she can forsee all attacks every once in a while and counter them with the same amount of damage you would've dealt to her for a few seconds.
Iadoa: Can freeze you in time for several seconds, cannot be stunned, and unless you have either the Chaotic Hourglass or the Dragonoid of Hours in your inventory, he can do a powerful Astral Shift attack that does massive amounts of damage.
Chaos Manticore: He can poison you, which does Damage Over Time that gets worse as the fight goes on unless cleansed with the water of the waterfall in the arena, and once you cleanse the poison, you cannot access the waterfall again for about 60 seconds.
Lionfang: Has a Damage Over Time effect similar to that of his Beast, only there's no way to cleanse the effect. In addition, his Essence Draining attack puts the stun on you for several seconds and cuts your damage and healing in half.
Megaman Battle Network 6. Colonel, Megaman's former ally in the previous game, who Megaman refuses to fight throughout the game until he realizes that words cannot get through to him. Among his new attacks is a finishing move that is used once your HP reaches a certain point. If it connects, you are instantly killed unless Megaman is equipped with Under Shirt.
Marquess Darin of Laus and Sonia Reed in Fire Emblem: The Blazing Sword. The latter is, bizarrely, completely optional.
Fire Emblem Awakening has three, each accompanied by a common boss battle theme: Gangrel at the end of the first act, Walhart at the end of the second act, and Validar just a few chapters before the end of the game.
The Arishok at the end of Act II in Dragon Age II. This victory earns Hawke the title of "Champion". This in turn makes Hawke the most important person in Kirkwall, which forces Hawke to take sides in the Mage-Templar conflict in Act III.
Marquis Elmdore and his bodyguards, Celia and Lettie. Alma is to be the vessel of Ultima.
Act IV: Dycedarg, your elder brother/Adrammelech. This is the end of Beoulve family.
Baten Kaitos seems to have an affinity for these: the first game has Geldoblame, Kalas, and the final fight with Giacomo, Ayme, and Folon; the second game has Guillo, Shananth, and Wiseman, though the last of those is actually hidden away in a sidequest.
Ornstein and Smough from Dark Souls. Epic music, extremely challenging, and takes place in a huge and grand hall. Defeating the pair is the final test before receiving your next major task after ringing the Bells of Awakening.
Shining The Holy Ark has you fight Rilix after you learn that the King is nothing but a puppet and that she plans to revive the thousand year kingdom. Oh, and she plans to kill you.
Xenoblade Chronicles: Egil, the leader of the Mechon. Then later the Disciples of Zanza.
In EarthBound, most of the problems in the Eagleland section (Onett to Fourside) was caused by the Mani Mani Statue sent by Giygas. The statue manipulated six people directly and large crowds though them and is finally confronted by Ness and Jeff in an illusion world it created. It's not a defenseless statue, though, and fights back. Destroying it lets everyone in Fourside manipulated by it go back to normal. Except for Pokey/Porky.
Mass Effect 1 allows you to come face-to-face with Saren on Virmire, right after you learn the true nature of Sovereign, the starship he's been using to wreak havoc around the galaxy and brainwash people to his will, along with its goals. He possesses powers from all three of the skill trees available in the game and is an example of Heads I Win, Tails You Lose, considering that no matter how much damage you do him he gets away scot-free, leaving you to make a Sadistic Choice on whether to save Kaidan or Ashley when you destroy his base.
Mass Effect 2 has the mission on the abandoned Collector ship featuring that game's Big Bad, Harbinger, whom you never directly confront but rather have to defeat his multiple drones which he can Villain Override. This isn't your first time confronting such an avatar, but that occasion falls under Wake-Up Call Boss. This is right after you learn that his plan for an Alien Abduction is considerably larger in scale than believed, and that the Collectors are all that's left of the Protheans.
Galaxy Angel — the first fight with Noa in the Black Moon's core.
Third Person Shooter
The Lupino Showdown from the original Max Payne, which has Max fighting roughly thirteen mooks that swarm in one after another after him before Jack Lupino himself makes his entrance with two of his personal guard and a sawed-off shotgun. He's also hopped up on drugs and completely insane.
Sin and Punishment has the battle against Kachua, which actually shares its battle theme with the final boss, and where Saki first transforms into a monster.
The second has the fight at the end of Stage 6, a lengthy, 3-stage ordeal, ending in a hand-to-hand fight, and ultimately resulting in one of the characters being knocked out, and the other transforming into a monster in order to storm the final level.