Last bosses are supposed to be epic, but the fact is they aren't always. Sometimes they're downright anti-climactic. Usually they're just challenging. But every now and then is a last boss that is absolutely epic. To make this list, they don't have to be hard, but you'll definitely have a sense of accomplishment having beat these fuckers.
1. Baby Bowser
Game: Super Mario World 2: Yoshi's Island
System: Super NES
When it comes to the Mario games, Bowser tends to be a bit of a let down, usually he's a wuss and beating him can be exciting, but usually it's over too fast and too easily. Not so in Yoshi's Island. Baby Mario and Yoshi arrive and the little bastard wakes up and flattens Kamek, then the battle begins. It's pretty easy, but for the second phase is when some serious shit starts going down. Kamek returns and uses his growth spell on Bowser, who becomes much, much larger than you. Larger than his castle even. Throughout the entire battle, Bowser is in the background and Yoshi has to throw giant eggs into the background, if he reaches you, you die. He also spits fireballs and makes the platforms you're on smaller. It's a tough battle and it's a great concept.
2. Mother Brain
Game: Metroid III: Super Metroid
System: Super NES
This one really has it's full effect if you have played the first two games, but even without that, it's still absolutely great. The battle begins the same exact ways it did in the original Metroid, with Mother Brain being simply a...brain. In a glass jar. You break the jar and pump missles into it until it's dead. Then...it comes back. The mother brain rears up and starts attacking you. The best part however is the fact that Samus can't win. And just when you're about to be blasted into oblivion the baby Metroid from Metroid II (who had attacked and spared you earlier) appears and attacks the Mother Brain. It loses, but it gives you enough power to annihilate this beast. It's a bit easy when you get down to it, but anybody who played the game knows this was and remains to be one of the most memorable end bosses in Nintendo history.
Game: Chrono Trigger
System: Super NES, Playstation, DS
There's very little in Chrono Trigger that isn't awesome, and Lavos is no exception. You initially face off against him in 12,000 BC, where he pretty much destoys you (you actually CAN beat him there, and you'll get a special ending for it, but that's kinda beside the point.) The most amazing part is he actually kills the main character, Chrono. At any point after this you can challenge Lavos for the last boss, but you'd be missing out on most of the game if you did, and you probably couldn't beat him. After a load of side quests, one of which offers you the opportunity to bring Chrono back and another offers you the chance to have your mortal enemy Magus join you, you're ready for round 2. Lavos does the cliche "mimick all the other bosses thing" but once you get inside his shell is when the real battle begins. The second and third form are absolutely amazing, and the third form, Lavos Core is probably my favorite last boss ever. With absolutely devastating attacks, the end of a great storyline and a kick ass musical theme, Lavos Core is the most fun part of an already great game.
Game: Dragon Quest VIII: Journey of the Cursed King
System: Playstation 2
Just look at that motherfucker. You know this is going to be some great shit. You fight his earlier form, then have to run out of the castle. Then you fight the castle. For the final stage, the godbird Emprea comes back one last time for an assist. The entire end battle has your party ridding on Emprea's back as she basically orbits Rhapthorne. This is because he's the size of of an asteroid. Getting rid of his shield alone (using the souls of the people he's killed) can be amazingly punishing, and the battle itself is epic. He'll throw meteors at you, bat you out of the sky and of course use magic. Beating him is no small task, and you get one of the best endings in a video game ever as a reward.
5. The Emperor Ing
Game: Metroid Prime 2: Echoes
Okay yes, technically you battle Dark Samus one more time after beating the Emperor. But beating her is part of the classic escape sequence and she can't hold a candle to Emperor Ing, the true end boss of MP2. This beast has around seven forms to go through, and usually there's more than one way to deal with things. Do you concerve your ammo and take the long road? Do you pack all your ammo into the annihilator beam and end it quicker? Or do you take a chance at one of the one-hit kills you can perform on a few of his forms (like one where if you're very lucky, you can screw attack right into his mouth.) No matter how you handle it however, Samus will have to use most of her abilities and it's going to be a long one.
6. Psaro the Manslayer
Game: Dragon Quest IV: Chapters of the Chosen
System: NES, Playstation, DS
No matter which version of Dragon Quest IV you're playing, this is a great battle. With this game, Enix invented the concept of the sympathetic villain in an RPG and Psaro was perhaps the best example of this. Psaro started off as a monster with human emotions who was in love with an elf named Rosa. Rosa had the unusual power to cry rubies, which caused many humans to try and capture and torture her. Psaro kept her safe in a tower, but eventually some people got ahold of her and killed her in a misguided attempt to get her tears. Psaro turned against humanity and uses "The secret of evolution" to transform himself into Psaro the Manslayer, who is your final battle. While it's true that the Playstation and DS versions added a sixth chapter, where you found out that one of Psaro's underlings betrayed him and sent people after Rosa, letting you resurrect her and bring Psaro to his senses, the battle with that guy is essentially a slightly tougher version of this one. Personally I love the original version and it's tragic ending (though the DS version is one of the best remakes I've ever played.) No matter which one you play though, you're in for a rough ride, as you'll need to use all 10 of your characters to beat this guy.
Game: Super Smash Bros. Brawl
Tabuu has no backstory and shows up near the end of Super Smash Bros. Brawl as the guy controlling all the villians, including Master Hand, Ganondorf, Wario and Bowser. The first time you meet him, he literally shows up out of nowhere and blasts all the characters at once, including his own underlings, turning everyone into trophies. King DeDeDe however knew all about this and had special badges that would turn him and Luigi back and along with Kirby and the rest of the cast as they get rescued, you eventually get to this guy. Sonic the Hedgehog even shows up at the end to break the guy's wings so he can't do that Trophy beam again. So the actual battle? It's great. You'll get six characters and unless you're already a pro and know the way to beat him easily (Charizard, Rock Breaker...) it's gonna be hard. I've fought him a bunch of times and every time he does an attack I've never seen before. Of course the worst of it is his circular beams, which will pretty much own you in one shot unless you roll at exactly the right time. Tabuu may be an archyptical winged blue guy with no backstory who shows up out of nowhere, but damn if the battle against him isn't great.
Game: 3rd Strike Street Fighter III: Fight for the Future
System: Arcade, Dreamcast, Playstation 2, X-Box
Gill is a bastard, but he's a damn great last boss. He can be hard bordering on unfair, but you keep pressing continue because you really feel like you did something after beating him. Gill is a big scary naked dude who's half fire and half ice, and he can pretty much slap you around any time he wants. In the original Street Fighter III he had the oh-so-fuck-you ability to fully resurrect himself if you beat him when his super art meter was full. In Giant Attack he could also call forth a meteor shower because that's totally called for when fighting some Karate guys. In 3rd Strike he gets the ability "Sepharic Wing" an unblockable attack that you can't parry and fills up the whole screen. Even with all this, Gill is beatable, but only barely so.
Game: The Legend of Zelda: The Wind Waker
Of all the Zelda last bosses, Ganon in The Wind Waker is the most epic, and probably the best. For once you fight the beast form once, get that out of the way, but the end is a great sword fight between Ganon and Link (so great they repeated the same basic premise for Twilight Princess). Hyrule Castle is basically in a big bubble underwater and then it pops. You're battling Ganon on the roof as an ocean cascades down around you, after just having your mind blown that your talking boat is the king of Hyrule. The setting, the battle itself, the fact that you team up with Zelda and the way it ends with Link's ultimate finishing move, a sword right through Ganon's head, the entire thing is just fucking epic.
Game: Guitar Hero II
System: Playstation 2
Free Bird on Hard or Expert is one of the most exhausting, epic and fun "last bosses" you'll find in any Guitar Hero or Rock Band game. It's pretty much the ultimate rock anthem, so much so that people love to shout the song's name out at concerts, and not necessarily Lynyrd Skynyrd concerts. It's long length, insane solos and the Stonehenge setting make this the best way to end a GH game.