In most games, and that too counts for RPG games, the final boss is a villain. Of course there is not good definition of "good" or "evil", and only a fool would even use these words are definitions, but I guess we all agree that Kefka from Final Fantasy VI is definitely evil.

Some final bosses are rather dubious on this point. Ghalleon from Lunar Silver Star Story for example. He originally meant well, but walked the path of evil in the end.

Please note, this list will not be complete, since I haven't played all jRPG games in existence. This is just a random pick.

I will describe the intentions of the final bosses in this list, so be warned that you WILL find spoilers here!!!

Myriah - Breath of Fire III

This one get people to frown. She masterminded a genocide and still she's not a villain. Yeah right, you think. Myriah is the protector Goddess of everything that lives, from a cute little fellow to the most dangerous monster. She loves life and vowed to protect it. The Dragons, or rather, the Brood, as the Dragons are called, have a power so great they could destroy all life with ease, and their power was even so great that they could threaten the existence of the world itself. Myriah simply feared this enormous power and decided to wipe out the Brood. The Brood however didn't fight back and that's how they became almost extinct, showing that the Brood did understand the responsibility their power gave them. Myriah was only unable to see this. When you face her, and Ryu decides not to give up his power as a dragon, Myriah sees him as a threat and thinks that killing him is simply something that has to be done in order to save the world. She's simply misguided.

The goodness of Myriah is shown all over the game nonetheless, though. She made sure that machines from the Techno Age were still being developed and that the people living today can make use of them. She did all she could to make sure civilization wouldn't perish. She is simply overprotective.

Fou-Lu - Breath of Fire IV

Fou-Lu might story wise be one of the best final bosses to ever appear in RPG history. The translation from Japanese is only not very good, and there was also a lot of censoring, so the dangers of misunderstanding him are pretty big.

In the world in which BOF4 takes place, a group of people brought forth Gods by summoning them. These Gods reigned over the world and eventually became dragons, and continue to watch over the world. Only a small tribe living in the hidden city of Chek know how to do this properly, and only they got the wisdom to do this with the correct intentions and to summon Gods without posing any dangers.

In these times there was also a world war. The people in the west had no knowledge of summoning Gods and tried to do it anyway, and summoned a God who would make sure there would be a world were there would be no war. Fou-Lu was summoned through this process. He led the people out of the war, and forged an empire in which they could live in peace. This became the Fou Empire. Fou-Lu reigned over this empire as its first emperor. However as the ones who summoned him were merely amateurs, Fou-Lu was cleft in two. Two bodies separated by distance and time. The other half is Ryu, who appeared over a thousand years later. Fou-Lu was therefore weak and could not reign forever as god. So he decided to sleep for a thousand years, so he could recover his strength. He formed a promise with the people that the people would live on in peace and that he would, once united with Ryu, lead them to happiness and eternal peace.

However once Fou-Lu fell asleep and was entombed, the horrible truth came forth. The Fou-Empire had become a very powerful nation. Not only that. Fou-Lu left them magic devices that made them even more powerful. And because Fou-Lu made people taste power, they began to thirst for more. And so a new war came. Now with the eastern nations of the world, who would later form the Alliance in order to be able to combat the Fou Empire.

When Fou-Lu finally awakened it became clear that the humans did not hold their promise. The fact that you can play Fou-Lu as a playable character gives you a good view on how things go. Emperor Soniel was not willing to give his power back to Fou-Lu and even sent out general Yohm to terminate him. Fou-Lu still gets to believe in the good of humans when Bunyan treats his wounds. Later on when he gets wounded again he's being treated by a female farmer named Mami, of whom it is safe to assume she was in love with him, and not only that. Although Fou-Lu knows that a relationship with Mami is impossible due to her only being a simple farmer without a clue of the world around her and he being a god with a far greater responsibility, it is clear he returned her affections. When Yohm arrests her and sacrifices her to the carronade, a kind of gun that shoots hexes made out of human sacrifices, solely in an attempt to kill Fou-Lu, his belief in the good of humans snaps, and since the humans did not upheld their promise he decides to destroy the Fou Empire, killing everybody living in it.

Fou-Lu's actions are merely the response of a God who's beyond himself in anger, and well, when we see how cruel humans treated him in their lust of power, I cannot blame him.

Hauser - Wild Arms 4

Hauser is the father of main protagonist Jude. He merely detected the damage the group of scientists he belonged to caused and wanted to fix that. He became a wanted man when his attempts to neutralize a very dangerous device in the city of Verklarung goes wrong, destroying the city killing nearly everybody living in it. Raquel Applegate is the only known survivor, although the word "survivor" is in her case debatable, as she got wounds due to it that cannot be healed, and which would eventually cause her to die young. Hauser was overcome with grief and wanted to do something to right his wrongs. On several occasions in the games he even helps Jude. When Jude and company crash into the remains of Verklarung, they all find their wounds treated when they wake up (which was Hauser's doing). Yulie being a paladienne she could do what Hauser himself could not, so he requests her to do it for him: Bringing the restless souls of the victims of the Verklarung incident to eternal peace. We can even see him taking care of a young puppy. When he gets arrested by the Brionac Forces, their leader, Lambda, taunts him in many ways possible. Hauser was already very angry about him being chased down like a wildebeast while he only meant to do good. Lambda even shows Hauser an empty dog collar implying that he killed Hauser's puppy. This was a bluff (as the puppy is later revealed to be still alive), but this caused Hauser to snap, and as he merges with a Wild Arm he completely loses control of himself, causing him to become the final boss of the game. Hauser was definitely an honest man, but a victim of human cruelty.

Volsung - Wild Arms 5

Volsung may be pretty debatable. In Wild Arms 5 there are two races on the world. The humans and the Veruni. The Veruni are treated as nobles. The humans as slaves. There is considered to be a huge "wall" between the two races. This didn't stop humans and Veruni to mate though, and Volsung is the child of a human and a Veruni parent. As a kid he was tasked to bring the two races together. He was desperate, as nobody was willing to listen to him. Evil spirits how died under the hatred of the two races eventually took possession of his body turning him into psycho homicidal maniac with no sense of remorse or compassion. When Dean and his friends ultimately defeat him he gets freed from these evil spirits and will eventually become himself again and as a result we see an entirely different Volsung. His presence on this list is therefore debatable... Did you beat Volsung, or merely the evil spirits inside his body?

Jecht - Final Fantasy X

A lot of debate goes on about the final boss of Final Fantasy X. Since Jecht is the last boss who can actively cause a "Game Over" screen, I consider him the final boss. Jecht is both a despicable as an honorable man, but certainly not a bad guy. Jecht is the best BlitzBall player the world has ever seen, and he was very well aware of that, and that turned him into an arrogant git. He was certainly also not very skilled as a father, causing a very weird relationship with his son Tidus, who eventually grew to hate him. Of course, a large part of the guilt also lies with Jecht's wife who was so devoted to him, that she easily neglected Tidus, causing Tidus to miss the love his mother should have given him, and not really seeing the love from his father, as Jecht was unable to express himself properly. When Jecht accidentally ends up in Spira and joins Braska and Auron on their quest to beat the horrible monster called Sin, Jecht is at first still the arrogant man we all came to hate, but as the journey goes on, Jecht begins to realize what a horrible father he had been for Tidus, and that despite all his talents as a BlitzBall player, the world does not circle around him. As he came to understand how the people suffered under Sin's terror and Braska's resolve to fight this, his good sight surfaced more and more, although he's still not able to express his thoughts well. When Braska needs to sacrifice somebody in order to fight Sin, the confirmation of Jecht being a good man comes when he offers himself as the sacrifice, in order to become Braska's Final Aeon, allowing Braska to beat Sin. He only didn't know that he would become the new Sin in the process. As Auron reveals pretty early in the game that Sin is Jecht we can see how Jecht desperately tries to reach out to Tidus in order to end the madness of which he is now part. He wants his son to kill him so he is free from the spiral of death. It is unfortunate that Jecht still has to assume his Aeon form once more in order to fight Tidus and his friends. However his greatest wish to reconcile with his son eventually comes true.

Quan-Lee - Grandia Xtreme

I was a bit conflicted about Quan-Lee. Quan-Lee is an artificial life-form created to rule the world as king, in order to end war forever. Quan-Lee however has no understand of a human heart and human emotions, which caused him to turn everybody into mindless zombies who would obey his will. With everybody being mindless, there was no reason to get in conflict, and thus eternal peace would be guaranteed. It's not that Quan-Lee had any evil intend. He only does not understand that emotions is also what we need to dream and be happy.

Vayne - Mana Khemia

This may be the oddest entry on this list, since Vayne is the game's main protagonist. But he is also the final boss. Vayne is trained to be an alchemist on Al-Revis academy. He has no knowledge about his heritage and lived as a hermit avoided by everybody. His only friend is his cat Sulper. His cat is believed to be a mana, and since alchemists often rely on the power of their mana, Sulpher is invaluable to Vayne, both as a mana, and as a friend.

It is later revealed actually that Sulpher is a normal cat and that Vayne himself is actually a mana. An artificial mana created by Theofratus, a very famous alchemist who was driven into madness when he could not save a girl from a terrible disease. He created the wish mana Vayne and wished himself dead. Vayne, being a very kind and humble person goes mad when he finds out and loses control over his own power as a mana, and unwilling creates an alternate world. It's here that Vayne will eventually have to be fought by his friends. Eventually he wishes to become a normal human and with his power as a wish mana he can make it come true.

Seraph Lamington - Disgaea

The Seraph is no villain, and actually not even the game's main antagonist (which happens to be Vulcanus, you fight before you meet the Seraph), although the game the Seraph played is far from clean, even with the best (and even wisest) goals in mind.

The Seraph is the leader of Celestia, the realm of the angels. He did see much prejudice towards demons among the angels and the demons were only too eager to return the prejudice. Hoping to end this he formed a secret bond with King Krechevskoy, the overload of the Netherworld, the realm of the demons. He sent Flonne to the Netherlworld with the task to assassinate the king, who was already dead, and the Seraph knew this due to his secret bond. It was rather a lame excuse hoping Flonne, how is a love freak, would be able to trigger some love in Laharl, who was destined to be the new overlord. Laharl had banished love out of his heart, since his mother sacrificed himself for him out of love. King Krechevskoy came as a secret helper to Laharl, disguised as Vyers, who is shamelessly renamed "Mid-Boss" by Laharl.

Things get messed up as Vulcanus interferes, who deems angels superior to everything. Vulcanus tries to sabotage Flonne's mission and even involved the humans in everything all to complete his own secret agenda, unaware of Flonne's true mission and the Seraph's true agenda. This however forces Flonne to break the angel law by killing angels. But we can't say the game the Seraph himself played was clear.

In the end Vulcanus is unmasked and punished, however as Flonne also committed crimes the Seraph had, according to protocol to punish her as well, which she willingly accept. Although Laharl refuses to admit it, he had fallen in love with Flonne. Flonne's true punishment was to become a fallen angel, and to be banished from Celestia, however in order to punish himself, he transforms Flonne into a flower, hoping Laharl would go berserk and attack him. This causes the final boss fight.

Depending on how you played the game, the Seraph is after the fight able to turn Flonne back from flower into an angel, but still a fallen angel. In a bad ending Laharl sacrifices himself to turn Flonne into a fallen angel.

Liezerota - Disgaea 5

Liezerota is the extreme goodness in every single way. I am actually thinking if her name is a translation woe or not. The Japanese language is a bit influenced by the Dutch language as a kind of heritage from the VOC time. The Dutch were one of the few Japan did business with in the time. Liezerota comes close to the Dutch girls name "Lieselot" or "Lieselotte". I've actually met a girl with that name when I was still a boy.

Liezerota, commonly called "Lieze" is the sister of the game's main antagonist Void Dark. The game's main protagonist is Killia, who was a very harsh overlord, with a heart as cold as ice. He tried to kill the master of martial arts, Goldion, but couldn't defeat him, and to his big horror, Goldion even took him in as his apprentice, and as such Killia got in touch with his son Void and his daughter Liezerota. Lieze acted very affectionate to Killia, originally much to Killia's chargin, but eventually, she managed to melt his heart a little. Void however was very overpossessive over his sister, and the entire idea of his sister giving herself to a man, was unthinkable. Void eventually tried to kill Killia for the involvement with Lieze, but something happened neither Killia nor Void expected. Lieze sacrificed herself for Killia taking the killing blow in his place. Desperate to keep his sister alive he performed many dark rituals over her and somehow managed to preserve her.

Killia was overgrown with grief over Lieze's death, and tried to block out his evil self completely since then... This costs terribly much energy, which is why he has to eat so much before combat. Eventually Killia had to overcome his evil self. After beating Void Dark, Killia finds her, however in an unconscious state. In an final attempt to keep Lieze away from Killia Void takes possession over her body, which transforms her into a dark entity thus igniting the final boss fight (all content after that is considered post-game).

Now she's not entirely in the same league as Volsung (mentioned earlier) who was also merely possessed. Volsung had no control at all while possessed, although after the spirits were driven out from him, he does appear to have memories from the time he was possessed. Liezerote is actually still partially in control and you can even hear her voice warning you to go away as she doesn't want to kill you, but she's unable to stop Void from trying to do so, thus her body still acts without her consent. Volsung did while possessed do many bad things over the course of the game. Liezerote does not. As a matter of fact, until the very moment you find her for the last battle, she was believed to be dead.