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Since Vanilla had no set main villain, I will include all of it's raids save for Ruins of Ahn'Qiraj. I will list most of the outdoor bosses, as well.
For Wrath of the Lich King, I will include two bosses from Ulduar alongside the Lich King, for importance purposes.
EDIT: Included one other Mists of Pandaria boss due to importance.
Be warned, this list is incredibly long.
Zul'Gurub - Hakkar the Soulflayer
Hakkar the Soulflayer was a Loa who corrupted and enslaved many of the trolls in Zul'Gurub.
Blackwing Lair - Nefarian
Nefarian was the son of Deathwing, and was the Lord of Blackrock Spire. He conducted horrific experiments, but ultimately met his (first) end in his own lair.
Molten Core - Ragnaros
Ragnaros was the elemental lord of fire. He was summoned by Majordomo Staghelm in the Molten Core without warning, and was pushed back into his elemental plane after being defeated.
Dream Portals - The Nightmare Dragons
Lethon, Emeriss, Ysondre and Taerar were four of Ysera's most trusted lieutenants. They were corrupted by a horrific being within the Emerald Dream.
Naxxramas - Kel'Thuzad
Kel'Thuzad was originally a mage from Dalaran, who had become a necromancer and later a Lich when risen by Arthas. He was one of Arthas' most trusted lieutenants, and ruled over Naxxramas before being defeated. He and Naxxramas later moved to Northrend.
Azshara - Azuregos
Azuregos was a trusted lieutenant of Malygos. He was tasked with holding a shard of the Scepter of the Shifting Sands, but was displeased with his task due to his interest in studying magical artifacts in Azshara.
Temple of Ahn'Qiraj - C'Thun
C'Thun was an Old God, who supposedly defeated a Titan. He created the Qiraji, and ruled over Ahn'Qiraj, though he was later defeated there.
Black Temple - Illidan Stormrage
Originally a night elf demon hunter, Illidan had become half-demon after absorbing the Skull of Gul'dan's power. After suffering defeat at the hands of Arthas, Illidan fled to the Outlands where he was later killed in his lair, the Black Temple.
Sunwell Plateau - Kil'jaeden
The current leader of the Burning Legion, Kil'jaeden was originally an Eredar who led his people alongside Velen and Archimonde. He joined the Burning Legion after Sargeras recruiting most of the Eredar, and attempted to invade Azeroth, using the Sunwell as a portal for himself.
Ulduar - Algalon the Observer
Algalon the Observer was the Herald of the Titans. After the watcher Loken's death, he came to Azeroth to ensure all was well. He was defeated in Ulduar, and ultimately helped to save the planet by giving the adventurers in Ulduar Reply Code Alpha after having a change of heart regarding the world's fate.
Ulduar - Yogg-Saron
Yogg-Saron was an Old God imprisoned in Ulduar by the Titans. He corrupted Loken, and soon after the rest of the watchers that kept watch over Ulduar.
Icecrown Citadel - The Lich King
The Lich King was originally Arthas Menethil, Prince of Lordaeron. He was the first known Scourge Death Knight, and became the Lich King after donning the Helm of Domination. He was the wielder of Frostmourne, and sought to wipe out all life on Azeroth.
Attack on Wyrmrest Temple/Dragon Soul - Deathwing
Deathwing was originally Neltharion the Earthwarder, the Dragon Aspect of Earth. He was corrupted by the Old Gods, and became what could be seen as a living weapon.
Pandaria - The Sha
The Shas of Doubt, Anger, Hatred, Violence, Despair, and Fear were the living manifestations of negative emotion. They were thought to be the remnants of an Old God, Y'Shaarj, who had died.
Heart of Fear - Empress Shek'zeer
Shek'zeer was the Empress of the Mantid, who was corrupted by the Sha of Fear. She was later killed by the Klaxxi and adventurers assisting them.
Throne of Thunder - Lei Shen
Lei Shen was the first Emperor of the Mogu. After delving into the Mogu'shan Vaults, he found a titanic watcher. Events unknown to many(and possibly all but Lei Shen and the Watcher himself) occured within, and Lei Shen emerged with unbelievable power, and created an empire. He later died of presumably natural causes, but was resurrected by the Zandalari.
Throne of Thunder - Ra-den
Ra-den was the titanic watcher who kept watch over the Engine of Nalak'sha. He was presumably defeated by Lei Shen, who had delved into the Mogu'shan Vaults.
Orgrimmar - Garrosh Hellscream
Garrosh Hellscream is the son of Grom Hellscream, and is the current leader of both the Orcs and the Horde itself. He seeks only to further empower the Orcs, and seems to care little for other races even within the Horde.
Isle of Giants - Oondasta
As the war against Lei Shen's island citadel began, Alliance and Horde scouts made an effort to intercept missives between the major Zandalari camps. One such exchange seemed to revolve around an unfamiliar Zandalari word, always surrounded by terms of conquest and power: Oondasta. On the Isle of Giants, the Zandalari Beast Ward raises it's might beast as an engine of war, and is putting the finishing touches on this Loa-infused monstrosity.
Edited by Wolvigar on 4/19/2013 6:10 PM PDT
Definitely Arthas and Kel'Thuzad for me. I've always been a huge Scourge fan ever since Warcraft 3. I was sad to see Azeroth's one true king fall at the end of Wrath. T_T
As for Kel'Thuzad, he was defeated at Naxxramas but his phylactery was never destroyed to the best of my knowledge... He may yet still be around. One can only hope.
Hm, "End-Game" boss makes me think final boss of the expansion's final raid. That'd just be Kel'Thuzad, Kil'jaeden, Arthas, Deathwing, or Garrosh. Of that group it's gotta be Deathwing. Even if his personality was kind of ruined in Cata, I still love his story and the schemer side of him.
If you just mean last boss of each raid, then Lei Shen is pretty awesome. It's a shame he had to go so soon.
Technically the quest to open the gates of AQ gave a storyline to why we go into Molten Core and Blackwing Lair, to acquire the items needed to rebuild the Scepter of the Shifting Sands. Sure it was a few patches late, but that's largely the reason.
Yogg-Saron. His mechanics were really fun; it was cool to be one of the few that wasn't driven insane. TBH, I haven't even fought him with one of the watchers assisting me.
First runner up is the Lich King, because his mechanics were also fun, and he was Arthas Menethil for crying out loud.
I didn't like Deathwing's fight at all. Its mechanics were kinda boring and the no more dragon aspects part really got me down.
I have to go with Kel'Thuzad in the original Naxxramas.
He had his original voice, he came in what was the most epic instance yet, and even if he WAS reused later, as a Lich this is kinda the central concept of his character.
Everyone else? ...
The Old Gods are a tired concept that have devolved into plot spackle for whenever Blizzard needs to kill a hole in the story.
Arthas was terribly miss handled, from execution to the very end.
Kil'Jaeden was... why the HELL were we fighting the Burning Legion's #2 guy this soon?
Ragnaros had no basis in lore deeper than WoW.
C'thun's concept was... If you want to do an homage to Lovecraft, do an homage to Lovecraft. If you want to do a knock off of the Zerg, do a knock off of the Zerg. But pick one...
Deathwing had to be retconned back to life.
Kael'thas was a horrible waste of the Blood Elves only meaningful character at that point.
Anub'arak was... poor Anub'arak. Poor, poor Anub'arak.
... really, I just have to stick with the original Kel'Thuzad.
"I always wanted to start my own religion... so I did!" ~ Kel'Thuzad
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