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Aoyama Masaya/Mark in Tokyo Mew Mew acts like the nicest person on the planet as a defense mechanism, and secretly hates humans while being unaware that he himself isn't human at all. He starts to see Ichigo/Zoey as "different" when she steps out of her comfort zone to understand him more — something she really doesn't want to do at first — and, by the end of the series, he sacrifices himself (and gets better) to save the entire world.
Ceres from Ayashi no Ceres starts out despising humanity (especially men) for what had been done to her in the past. As the series progresses, Ceres learns that humans aren't evil, just flawed, and her faith in the human soul was restored from watching Aya and her friends and loved ones.
Doctor Manhattan in Watchmen, though for him it's Humans Are Boring and Predictable. When the Silk Spectre finally breaks down upon realizing the Comedian is her father, he realizes that Humans, against all improbability, managed to live - and that's more than enough to realize that Earth needs him.
The High Evolutionary's plans to wipe out humanity were once waylaid by the Hulk's determination to survive in spite of everything.
In Grimm Fairy Tales, the Wicked Witch Belinda shows her friend Sela around a beach and explains that Humans Are Bastards by pointing out Jerk Jocks who bully others, a shallow girl who Really Gets Around, etc. When a building collapses, everyone Belinda pointed out immediately rushes over to help. The jocks use their strength to clear rubble and pull people to safety, and the shallow girl turns out to be a highly qualified doctor. Belinda gets disgusted and leaves, but Sela is amazed and is so touched that she decides to help too.
Manchester Black goes through a darker variant of this after trying and failing to provoke Supermaninto killing him. When Superman remains dedicated to his principles even after Black apparently killed Lois, Manchester realized that true heroes like Superman really did exist. This also leads to Manchester realizing that he had become just another supervillain. After erasing the knowledge of Superman's identity from the minds of the villains he granted it to in the first place, Manchester promptly killed himself.
In The Fifth Element, Leeloo loses her motivation to save mankind after witnessing its in-fighting and learning about its war-ridden past. However, Korben manages to restore her faith in humanity with The Power of Love.
In The Dark Knight (2008) The Joker has put two bombs in two ships, one of them full of convicts, the other full of ordinary people. The people on the ships are informed that they can detonate one of the ships and save their own lives. Of course, everyone immediately wants to blow up the other ship, but they hesitate, not sure whether this is the right thing to do? Finally one of the criminals orders one of the guards to give him the remote, telling him: "I'm going to do what you should've done ten minutes ago." After he gets the remote he simply throws it outside the window and returns to his seat. In the other ship meanwhile one man also wants to have the remote, because "after the all the people on that other ship are criminals and they deserve to die anyway". As he stands there with the remote in his hand he suddenly gets a change of heart and after a long hesitation decides not to go through with it. Later The Joker is surprised that none of the ships have exploded by now, but Batman tells him that he underestimated the people's sense of humanity.
Jean Valjean, in Les Misérables, after being put in prison for almost twenty years for a minor infraction, is wandering the streets of a small town looking for somewhere to spend the night after a day in which nobody will pay him full wages or rent a room to him because he is a convict. Nobody will let him even stay on their stoop, but one person points out the door of the local bishop. He is given pride of place at the bishop's table, a room for the night, and respect as a fellow human being. However, this trope doesn't take effect until he steals the bishop's silver and makes a run for it, and instead of denouncing him to the police, the bishop actually gives him the rest of the silver as a gift. Cue Heel Realization, My God, What Have I Done?, and redemption. Valjean goes on to become one of the most benevolent and just characters in fiction.
In Smallville, Clark usually regards himself as human, but when something makes him doubt it, Chloe is always there to pull him back.
Inverted and then subverted in House. House has a deep faith in the negative attributes of humanity. His favorite phrases are "everybody lies" and "people don't change." Cameron, and later Thirteen, try to prove him wrong whenever possible. However, just about every patient House has lied to him and usually also the patient's family.
Doctor Who: The Doctor is an...interesting case. He'll occasionally go on a very vehement Humans Are the Real Monsters phase, calling them violent, selfish and stupid, and then, something will happen (usually sparked by his companion) that restores his faith in them. After all, there's got to be a reason he hangs out on Earth so much.
It's actually discussed in the much darker Torchwood: Children of Earth with Gwen, who reminisces about when Jack used to tell her about the Doctor, and wonders why he sometimes just fails to appear, mostly around atrocities committed by humanity itself. She concludes that it is during those times that Humanity so utterly disgusts the Doctor that even he must look away. This has never been confirmed however.
In the Mork and Mindy episode, "Mork the Gullible," Mork is talked into freeing an escaped criminal who claims that he just needs to visit his sick mother and will return to turn himself back in afterward. Sure enough, Mork is arrested for freeing him and Mindy tells him that it is obvious that the crook took advantage of him and won't be back. In a genuinely moving moment, Mork tearfully agrees that he can't trust anyone again, until the crook suddenly returns as promised to turn himself in and get Mork released. With that, Mork's innocence is restored.
One Bloom County strip had Opus wallowing in gloom, thinking he's lost the Christmas spirit forever. Portnoy appears and gives him a gift which turns out to be plastic dog-vomit. Opus hugs him, saying in total sincerity: "Thank you. You've pulled me back from the brink. I'll cherish it forever." Cue Portnoy wallowing in gloom.
The World Ends with You: The Conductor, Kitaniji, was trying to achieve Instrumentality so that the Composer, Joshua, wouldn't destroy Shibuya. After all, people in Shibuya are self-centered and uncreative. But Neku, former poster child for cutting himself off from society, has learned about The Power of Friendship, so...
Tales of Symphonia: Dawn of the New World: Richter's plan, and every evil scheme leading up to it, was to find a way to seal off Niflheim without Ratatosk's help, so he could kill Ratatosk without dooming the world. Because Ratatosk wanted to Kill All Humans (and elves and mixes) because they've been causing problems for mana. But Ratatosk has been posing as Emil the entire time, and he's met Marta and the others, and decided that they're not so bad...
Duke in Tales of Vesperia initially intends to sacrifice the lives of every single human being in the world (Himself included) to destroy the Eldritch Abomination that's threatening its existence, feeling the world would be better off without them. After the party shows him their firm resolve by defeating him, though, he ultimately decides to help them with their plan to destroy it instead, which while still requiring sacrifice, doesn't involve any loss of life.
In the Sam & Max: Freelance Police episode "Reality 2.0", the internet has lost faith with all living things as Sam and Max infect the whole net with a computer virus, and the final puzzle in the game involves finding something called "respect for all living things" before the internet erases itself.
In Shin Megami Tensei: Strange Journey, resurrected Commander Gore has received the power of supernatural insight, or "brilliance," from the Schwarzwelt. Upon briefly returning to the Red Sprite in the Neutral Path, he assures the crew that he has seen into humanity's future, and —despite having been revived and manipulated by the forces behind the Schwarzwelt— he implies that humanity can improve itself and prevent its self-destruction if given a chance to survive.
In Shin Megami Tensei III: Nocturne's "Resurrection" Ending, Miss Takao, who started the game thinking humanity could no longer advance and needed to be wiped out for the world to advance, has come to realize the foolishness of this line of thinking. Whether humanity continues to stagnate, or whether it actually improves itself after the old world's resurrection, your example has given her faith in the possibility of the latter, and she'll never wish for humanity's destruction again.
The storyline conclusion of Pokémon X and Y comes after facing the Elite 4 and the Champion, when the player character is confronted by the immortal warrior-king of ancient Kalos, an embittered, nihilistic Death Seeker who wants to know what it is you fight for so passionately. Naturally, the correct answer to this question is to sicc your Pokemon on him, and the aftermath of that battle not only restores his faith in humanity, but also that of his runaway Floette, who decides it's finally time to forgive and return to her master.
In Dragon Age: Origins, if the Warden takes the time to befriend Shale and help uncover her forgotten memories from her pre-Golem life as Shayle Cadash, she eventually comes to see organic beings as not completely worthless. At the end, she even can admit to the Warden that she's interested in seeking out a way to become a Dwarf once more.
InQuest for Glory IV, a paladin can do this for Dmitri (whose grandfather, a famous paladin, had allegedly abandoned his fiancee) by showing him proof that said grandfather had not run off and had instead been killed fighting the undead. "I did not believe you before when you said you were a hero, because I did not believe that heroes existed. Never was I happier to be wrong."
In Hatoful Boyfriend, the Bad Boys Love route reveals that this was why the heroine was attending a boys' school for birds in the first place, to prove to the sapient birds that humans could coexist peacefully with them.
In the Tokimeki Memorial series, this is the storylines of Kaori Yae (in 2) and Taku Komori (in Girl's Side 2) in a nutshell. Thanks to their relationship with their respective games' protagonist, they get to realize that there are trustworthy people out there, and as a result they gradually open themselves to others. Takafumi Wakaouji in GS2 also claims in his ending that the heroine has restored his faith in humanity, although this seems to be a bit of an exaggeration.
In Gargoyles, human ally Elisa Masa helps to restore Goliath and the Manhattan Clan's faith and trust in humanity after they had been betrayed by humans who destroyed their home and their people.
Taken Up to Eleven in Ben 10: By the time Ben met Azmuth in "Secret of the Omnitrix", the scientist had completely given up on the whole Universe, to the point that he was willing to let it, along with himself, be destroyed. However, after seeing Ben in action, he has a Heel Realization, helps Ben win, and becomes more rational in later episodes.
The St. Valentine Day's Massacre: During the 1920s Al Capone was almost seen as a superstar by many people, who knew he was a gangster but felt he was somewhat above the general corruptness of society. Since nobody actually saw him commit any crimes himself and judges always declared him innocent he came across as a lovable Magnificent Bastard. That is until the St. Valentine Day's Massacre occured in 1929. Capone's thugs had disguised themselves as policemen and shot several other gangsters in cold blood. The news, and especially the photos of their bloody bodies, shocked the nation and reminded them again why Capone was actually not to be admired. Capone's image never recovered from this public backlash and he was eventually put in the jail.
During World War II some Jewish people had hid themselves in an attic to hide from the Nazis. One night they heard intruders in their hiding place so they kept quiet. Unfortunately it were indeed German soldiers investigating the place and one of them did open the attic door. When he saw the Jews there was a moment of awkward silence and fear, but then he simply shouted back at his fellow soldiers: "I see nothing upstairs either", closed the attic door and left. All the Jewish refugees in that attic managed to survive the war thanks to the unsuspected humanity of this one Nazi.
The Battle Of Solferino (1859) was one of the bloodiest battles ever. No mercy was shown among the soldiers, who slaughtered each other and left the wounded ones to die off alone in agony. Yet one witness was so shocked by this bloody aftermath that he founded an organization that could take care of these victims, while remaining neutral about the conflicts themselves. His name? Henri Dunant, founder of The Red Cross.
As awful as World War II was, with all the genocides and mass killings, it did produce several laws and organizations in order to provide humans with an official, legal confirmation of their basic human rights: The United Nations, Unesco, Unicef, the Universal Charter of the Rights of Man, The World Health Organization, The World Bank, The International Court of Justice, the World Food Programme,.. War crimes are officially punishable since these declarations came into effect. The European Union was also created as a result of World War Two to maintain peace and economic collaboration between all its member states, thus ending all wars that have been fought in these countries for centuries.
The Watergate scandal might never have been uncovered if one White House member didn't step forward to help the investigative journalists Woodward and Bernstein with solving the case. Nicknamed "Deep Throat" this member couldn't take the corruptness inside the White House any longer and decided to bring it all to an end. As Richard Nixon faced impeachment the entire believability of the United States and the Presidency was at stake. Yet Nixon decided to put the nation's interests before his own benefits and abdicated.
German general Erwin Rommel fought for the Nazis during World War Two, but was generally admired for being a decent human being who respected his prisoners of wars. He was even involved in plotting against Hitler to stop his ongoing atrocities, but the assault failed and he was executed. The very idea that even a high ranking official in an ethically despicable ideology and regime would keep doing what was fair and good for his fellow man and even resist orders from his superiors is amazing.
Similarly, Mikhail Gorbachev became leader of the Soviet Union in a very oppressive and restrictive system that would make it impossible for people like him to rise to such a high political position. He was an advocate of social changes for all people behind the Iron Curtain and even managed to put all these more human laws into effect, thus eventually causing the USSR and the entire Eastern Bloc to collapse in an almost peaceful way.
Joseph McCarthy's witch hunts against communists during the 1950s made his position almost untouchable. Not many people dared to question his tactics and general paranoia, which ruined the careers and reputations of many people who would normally be protected by the United States law to have free expression. Yet Edward Murrow, a journalist, risked his entire career by directly challenging Mc Carthy's ethics and methods. His bold stance worked and soon the senator and the general anti-communist climate was deemed unconstitutional and caused his downfall.
The single most unbelievable act of humanity occurred on Christmas 1914, when both German and Allied troops decided to have an armistice for one evening. They celebrated Christmas together and even played a game of soccer in the fields.