Acro is constantly loved and flapped around by birds. These birds even attack Phoenix when he starts accusing Acro of murdering the ringmaster (he did, but he was aiming for someone else). The birds desert Acro when he's at his most intense, but come back afterward.
In the third game, Dahlia Hawthorne is similarly accompanied by a trio of butterflies most of the time. Said butterflies explode when Dahlia's true nature is revealed.
The second Investigations game has Souta Sarushiro/Simon Keyes, an animal tamer from the same circus as Acro. His complete and utter love for the animals around him convinces everyone — Edgeworth included — that he's innocent of the murder in the prison. He’s the client for the second case, so Edgeworth has to defend him. It's all a facade. He has absolutely no sense of trust in anyone except for a single assassin and his seeing-eye dog. Everyone else is just someone to be used to get his revenge on the conspiracy that ruined his life, and his breakdown at the very end of the game reflects that with all the animals beating him up. And while techincally he's not lying about not being the killer for the murder in the prison, he most certainly manipulated the real killer into taking action.
Played straight with a defendant and heroic cutie Sasha Buckler from Dual Destinies. She adores every creature and has a sweet bond with the whale, which she adorably sings to sea shanties, uses an anchor-shaped whistle to issue tricks to her whale, and even wears arm floats when she can swim. Also played straight with her equally pretty predecessor, Azura Summers who is shown using a whistle to sing with her whale friend. Then there's her boyfriend who is another seemingly Nice Guy culprit. Of course there's the fact he never actually killed the victim and the supposed murder was a total accident, not to mention, he does genuinely like all the animals in the aquarium save for one orca he blames for the death of his girlfriend, the aforementioned Azura. He later makes amends with that orca when he learns Azura actually died due to the heart condition she had. So in a sense he's somewhat Double Subverted.
Rapunzel is this in the Dark Parables series, being the blessing conferred upon her by the nature goddess Flora. She not only gets along with everything living, but she has Swiss-Army Tears which can heal all injuries, and is immune to the Enemy Of All Living Things powers of her little sister Belladonna.
Darkstalkers: B.B. Hood is a funny case — plants sprout around her, and butterflies and moles like her far more than is normal, but she does not get along with wolves. (It should be noted that she has a lot of "cute" traits and a less-than-cute personality.)
The eponymous protagonist of Dropsy. Humans see his monstrous appearance and are convinced he's a Monster Clown (he's not), but animals generally like him and trust him implicitly — indeed, his dog and the other two Loyal Animal Companions he picks up during the game are necessary to solve puzzles, and Dropsy cares for them in turn. Dropsy also seems to be able to understand their speech, though he is mute himself.
The player character in the Endless Ocean games is this, as he/she befriends and learns about various sea life by petting it. The second game subverts it a little by allowing you to get attacked, but you defend yourself with a stun gun which explicitly has healing properties rather than anything lethal.
In Fable if you get your good rating high enough, butterflies start flying around you. If you get your evil rating high enough, flies do the same.
The "Animal Friend" perk in Fallout makes you this (somewhat). The first rank of it makes it so animal enemies won't attack you. The second makes animals attack enemies (except other animals, which they already do anyway making the 2nd rank practically useless).
Hermes, before he became Fandaniel in Final Fantasy XIV is a tragic example. He loves all his creations in Elpis, and is incredibly distraught when his fellow Ancients decide which lives or dies. When one of his creations, Meteion, reports that every star in the universe her sisters visited is either dead, dying, or destroyed immediately upon arrival and snaps, Hermes himself becomes overwhelmed by existentialism and allows Meteion to escape to the edge of the universe, kickstarting the conflict of the main storyline of the first eight years of the game.
Henry from Fire Emblem: Awakening. He is even able to communicate with animals and plants alike!
The Legend of Zelda: A Link to the Past: The ghost in the Sacred Grove is seen playing his ocarina for group of forest animals, who disappears if Link goes near him; causing the animals to scatter.
Though Saria is from Kokiri Village, she can often be found deep in the surrounding forest, near the Forest Temple, where she teaches Link her song. She explains that it allows her to communicate with the spirits in the forest and also allows her to speak to him telepathically. Which how she learns of the disturbance in the Forest Temple when she finally awakens as the Forest Sage, 7 years later.
Malon the ranch girl adores the horses under her keep and even endures Ingo’s tyranny because she fears he’ll hurt the horses. Malon is the only other character besides Link who can tame Epona.
The Legend of Zelda: A Link Between Worlds: Gulley, the young son of the blacksmith, is often confused as to why his wild animal friends tend to run away whenever anyone else approaches them. This is fitting, as he's an expy of the flute boy from A Link to the Past and is implied to be Saria's successor as the new Sage of the Forest.
The Cultists of Majesty combine this with Fluffy Tamer. They immerse themselves in nature as part of their religion and routinely patrol monster lairs, not to raid them but to charm the ferocious animals that emerge from them.
Amaterasu, the main character in Ōkami. Not only do animals adore her, but she also makes flowers bloom wherever she steps. She's a Physical God though, so it only makes sense. Nor is it one-sided — she will stop any time, anywhere, to feed the animals she encounters on her travels, whether rabbits or tigers. And when you make flowers bloom near animals, they get hearts over their head and run over to Amaterasu to nuzzle up to her.
N from Pokémon Black and White, a male example and probably a deconstruction, as he was deliberately conditioned into this through brainwashing and social maladjustment by Ghetsis. He never uses the same team of Pokémon twice, because he doesn't even capture them: he makes friends with wild Pokémon that can be found in the area and asks them to battle for him. He also has the ability to understand what Pokémon say. He then releases them afterward. In the sequels, Pokémon Black 2 and White 2, it is possible to obtain the Pokémon N released for yourself, and they all have maximum happiness. He also states in the sequels that he wants to use his abilities to become a mediator between humans and Pokémon.
In a sense, all the player characters in the games could count, since every Pokémon that can be obtained in the games can easily become a potential ally. Something that doesn't seem to come as easily for NPC characters. This is also kinda enforced by the game mechanics, as there are numerous ways to increase the friendship points but only exactly two ways (letting them faint in battle and spamming them with bitter herbal medicines) to reduce it.
Bear Hugger from Punch-Out!!, if his interactions with his bear and squirrel◊ companions are anything to go by. He even brings the squirrel along for his rematch, complete with little boxing gloves of it's own, and coos over it when he wins.
Erana from the Quest for Glory series is a powerful mage whose goodly influence you will come into contact with throughout all of the games. Several gardens have sprung up wherever her magic is at work, causing animals to gather and exerting an influence of calm and purity over everything.
Sakura Wars: So Long, My Love's Diana has a specific bond to birds; they flock to her and she can't stand to see them harmed, and faints when served Fried Chicken at a Harlem Church. Coqulicot from the third game lives in a circus and has this sort of relationship with the animals under her care.
Mono from Shadow of the Colossus. She's got the birds and fawn and everything. Even the squirrel looking up at her.
In The Sims 3, if Sims have the Animal Lover trait, they instantly qualify. One Sim in Appaloosa Plains(who fittingly enough has the last name Shepherd) is friends with all the playable pets in the game when it starts, and she has the Dog Lover trait instead.
Sonic's initial reason for fighting Eggman was to save his animal friends who had been captured and used to power Eggman's robots. In the end of the first game they are seen frolicking through the Green Hill Zone with him. Most of his friends have shown signs of this at least once too. Justified somewhat as they're animals themselves.
Subverted by Metal Sonic in Sonic the Hedgehog 4: Episode Metal. He goes through the same levels as Sonic all while freeing animals by destroying the robots they're trapped in (robots made by his own creator), much like Sonic would; but he's only going through them to track down Sonic and because they attack him first. Once he's found Sonic, the animals he's unintentionally freed jump happily around him, but he gets annoyed by this and scares them off.
Princess Kenny in South Park: The Stick of Truth has two abilities that call on animals. One calls a unicorn, and the other involves him singing to summon a swarm of rats. He is a princess, after all. The trope is parodied if the player messes up the action commands they have to do to make the abilities work, however, and can result in Kenny being impaled by the unicorn or devoured by the rats.
Reimu Hakurei, the main protagonist, has shown to feed wild animals by hand, summon birds via whistle, and when the fairies tried to trick her into walking into a lake fish spontaneously formed a bridged under her feet.
Kasen Ibara, the one-armed, horned hermit, has several exotic pets, and handles all animals well.
Warcraft: In World of Warcraft, there is a Druid only glyph by the name of "Glyph of Charm Woodland Creature", which "Allows the Druid to befriend an ambient creature, which will follow the Druid for 1 hour."
Yes, Your Grace: Princess Cedani is natural at taming wild animals, with her record by the end of the game consisting of a snail, a hedgehog, a fox and a bear cub. Unfortunately, she's also a Chronic Pet Killer and the last of the list is the only one that can potentially still be alive by the end of the game.
◊ companions are anything to go by. He even brings the squirrel along for his rematch, complete with little boxing gloves of it's own, and coos over it when he wins.
