Namely, almost every final boss in a Mario RPG, with the exception of Paper Mario, though he has a tendency to be involved in some way, especially in the Mario & Luigi series. They tend to be sequential...
M. Bison (OF COURSE!) in Street Fighter II. Even when the subsequent installments allowed you to play as him, you still had to fight a palette swapped version in a Mirror Match. The first two Alpha games subverted this by only making Bison the final boss for characters whose back-stories and motivation were tied to him (i.e: Chun-Li, Charlie, and Rose). Alpha 3 plays this straight by making the "Final Bison" variation of the character into the final boss for everyone except himself and Evil Ryu.
Dr. Robotnik in the Sonic the Hedgehog games. Specifically, he appears as a Recurring Boss throughout the game, until he finally attacks Sonic with the most powerful weapon, robot or vehicle at his disposal. As of Sonic Adventure, however, it has become increasingly common for him to be hijacked by an original villain.
Rugal Bernstein in The King of Fighters '94, '95, '98, and '02 (not to mention his son Adelheid in '03). The creators of the series admit that he is their favorite boss so far, which is why he's been used so much.
And before that, Geese Howard, even to the degree he he appeared as the end boss of a different game, and introduced said characters to KOF. Bam. Even got better from falling off of a building!
Dark Matter in three of the Kirby games, although King Dedede has a better track record.
Metroid has had many memorable bosses throughout the series, but most of them aren't final:
Mother Brain is the final boss of the original. She comes back in Super Metroid and then Turns Red. The Aurora Units (including the final boss A.U. 313) in Metroid Prime 3 are certainly shout outs to her.
Ridley is The Dragon in most games. When he isn't, he's a Recurring Boss. The one sort of exception is in Zero Mission, where a robot based on him is the final boss.
And even then, he sort of comes back as Ridley-X (X-Parasite that got a hold of Ridley's DNA)
The titular Metroid creatures usually aren't final bosses. Exceptions are the Queen Metroid in Metroid II and the Omega Metroid in Metroid Fusion.
Metroid Prime, later known as Dark Samus, in the Prime subseries.
Dark Force (or Dark Falz) in the Phantasy Star games; in Phantasy Star IV, the various "Dark Forces" are revealed to be incarnations of "The Profound Darkness."
Giygas in the first two Mother (Earthbound) games. Something that appeared to resemble Giygas was presumably going to be used as a boss in Mother 3, but was cut for unspecified reasons; it still exists in the game data, and can be viewed with a bit of hacking. It is creepy.
Big Boss in Metal Gear and Metal Gear 2: Solid Snake; later inverted in Metal Gear Solid 3: Snake Eater, where you play as the future Big Boss and your FinalBoss is... well, The Boss. Not coincidentally, Big Boss would leave the Patriots and split with Zero over his view of The Boss' dream, while the Final Bosses of the other three Metal Gear Solid games would overtly link themselves to Big Boss and claim to be fighting for dreams similar to what they thought he was striving for. (Although in MGS 4 there is the Liquid Ocelot switcheroo, where Ocelot was loyal to Big Boss to the point that he supplanted his own personality with that of Liquid... who may have not entirely shared Ocelot's vision of Big Boss' dream.)
The fight against Ansem-Heartless actually, Xehanort from the first game has freaking' 5 phases! First, he just fights you, while floating, then, he summons Darkside to kill you, next he fights you again, but you're alone, and he's faster, then, he goes One-Winged Angel and you have to fight him alone, next you have to gather your party again and take his One-Winged Angel form on once more. Then. He's. Finally. FINISHED!!!
Ten phases, actually. You didn't count the three times you fight Heartless in a void, the giant face on the ship, and the shield generator.
Marlurxia, the flower-fanatic Final Boss from Chain of Memories is not much better, he's even got three separate pieces of battle-music for his forms.
Then came Xemnas and this troper stopped counting phases. This was One final battle that could easily be called "evening filling": Epic stunts on sky-scrappers, a spaceship-kidnapping and Riku actually PLAYABLE (as in: you can run around as him) and that all in one Final Boss!
Seven phases. Slicing buildings, cannons, core, first Xemnas, dragon, second Xemnas, final Xemnas.
There were two more forms the creators actually scrapped.
And in Days, there's Xion, who has 4 forms, each of whom you fight in different worlds, with the final form being the size of the Twilight Town clock tower.
Ace Combat 04 and 6 subvert the trope, while Zero follows it: in 04 and 6 your final mission involves the destruction of a superweapon, Megalith and the Chandelier respectively; in 04, you can ignore Yellow Squadron and the S-37A ace altogether. In Zero however, the superweapon V2 is being controlled by Pixy from inside the ADFX-02 "Morgan" fighter, which is the final boss.
Although it's not technically the Final boss (The Big Bad jumps into its cockpit before the fight begins), the End Boss of zOMG Chapter One is definitely worthy of it's position. It's taken some crews hours to beat it. Not counting the hour or so it takes to get through The Very Definitely Final Dungeon (Of Chapter One).
It's actually gotten easier, since the game is still in beta and is prone to constant rebalancing, but even at its easiest the time and effort that go into beating this boss are impressive. Perhaps its strongest hour was in the second week of the game, when the 'body' stage had an attack so strong, the only known way to survive long enough to take it out was taking advantage of its AI to have it target a player out of reach and ignore the rest of the crew. And that's the fourth stage out of five; the 'head', which spawned deathmines and gunned down the strongest players like flies, was impossible to survive without a frenzy of constant healing and buffing. After that, the damage levels were turned down a bit, in exchange for an absurdly high regeneration rate... did I mention zOMG is marketed a casual MMO? This troper doesn't know whether to be excited or terrified to learn what the next chapter's final boss will be like. Say what you will about Gaia Online, but when they set out to make a final boss, they make a final boss.
Within the Halo series: Tartarus in 'Halo 2' and 343Guilty Spark is the pseudo-final very anticlimax boss (which still serves to be a Crowning Moment Of Awesome for many) of 'Halo 3'.
Andross in Star Fox and Star Fox 64 and Star Fox Adventures. After finally being defeated, his nephew Andrew tries to carry on the family, um, name, but he's just as incompetent as he was in Star Fox 64 and gets beaten in the very first level of Assault.
World of Warcraft, like most other MMORPGs, is loaded with dungeons, each of which has sub bosses and an end boss. However, the original game and expansions each has a Very Definitely Final Dungeon and a Final Boss, based on the Sorting Algorithm of Evil used to scale up the difficulty of the encounters. The Final Boss has, thus far, not been accessible at the launch of the game/expansions, being added in later content patches. They are, in order, Kel'thuzad in Naxxramas (the original version); Kil'jaeden in Sunwell Plateau (The Burning Crusade); and the Lich King, Arthas Menethil, in Icecrown Citadel (Wrath of the Lich King). Also see Giant Space Flea from Nowhere for more about Kil'jaeden.
Europa Universalis doesn't really have a Final Boss of course, but given their wealth, size, manpower and tendency to eat most of Germany and the Netherlands (giving it more of the above) comments have been made that the end-boss in EU3 is France...
In Cave Story, the final boss quartet of Misery, followed immediately by The Doctor, followed immediately by Red Flower Raging Doctor (or OMG There's So Many Freaking Bats Doctor), followed immediately by the dreaded Undead Core. With no chance to heal, except by picking up the health power ups that Misery's bat minions drop sllooooowwwwly. Typing this brings up unpleasant memories of trying to beat the Pokémon Elite Four without using items.
And that's not even the Perfect Run Final Boss. To get to Ballos, you need to complete a series of obscure requirements, the most important of which is ensuring that Curly Brace survives the boss battle with the Core. Then you have to defeat the final boss quartet, then you have to go through the Bonus Level Of Hell, and then you have to fight a massive multiphase boss made of pure Nightmare Fuel, all for the perfect, true, happy ending. It's totally worth it.
Although, arguably, it's actually Sarda, trying to get revenge on the Light Warriors for ruining his life when he was a child (don't ask; there's time travel involved), and White Mage for creating the universe before he could (after growing up and learning magic, he tried to travel back in time to create it himself, but wound up there four seconds too late and had to wait out fourteen billion years alone in the void).
Although now that Sarda has channeled Chaos, maybe the ending will be more like the game than readers expected. We'll have to see.
Although Pokémon Stadium has no plot line, beating all the stadium cups and gym leader castle makes Mewtwo appear above the stadium, whom you can fight. He is level 100, has godly stats, and a powerful move set. You WILL need all 6 of your Pokemon to come close to victory. Beating him can be considered a final boss since the credits roll if you win and it unlocks Round 2, where you get to do all the challenges again, but they are much harder. Beating the challenges in Round 2 makes Mewtwo appear once again, but this time he replaces a move with Amnesia, which pushes his super high Special stat beyond ridiculous levels!
Pokemon Stadium 2 ups the ante with Rival, who has similar requirements to face, and brings not only a super-powered lvl 100 Mewtwo to the fight, but he also has lvl 100 Lugia and Ho-oh along for the ride as well! And, just like in the first game, beating him unlocks Round 2, with a similar result as the first game when you finally beat all the challenges a second, far more brutal time.
Each set of games also has it's own "final" boss, or at least a boss who is crazily strong.
Red/Green/Blue/Yellow and the remakes Fire Red/Leaf Green all have Blue as the strongest battle-able trainer.
Gold/Silver/Crystal and presumably the remakes Heart Gold/Soul Silver all have Red, the protagonist in the above games, as the strongest opponent.
Ruby/Sapphire/Emerald have Steven, who gets a major upgrade in Emerald.
Diamond/Pearl/Platinum have Pearl, the player's rival, as the strongest trainer. In the last game, he has second-strongest team yet fightable in normal gameplay, his strongest Pokémon hitting Level 85 (surpassed only by Red's Pikachu in Heartgold and Soulsilver).