1. Legion (Mass Effect 2/3). It was such a twist to find that this geth - a major antagonist in the first game - had been following Shepard, not to kill him, but to join him in his fight against the Reapers. Legion basically was more intelligent than most geth due to a host of geth that made his physical platform work (prompting the name "Legion"), and he raised so many questions on what could be considered to have a soul. Asimov would've had a field day with Legion, and ultimately - in the best outcome where you spare both quarian and geth - he sacrifices his own life, just when he gained full sentience and fully realizes what it's like to die, to give the rest of the geth full sentience to help join the fight against the Reapers. He's my favorite Mass Effect character - out of a cast that includes Wrex, Drack (don't shame me for liking Andromeda; I loved it), Mordin, Tali, Garrus, Liara, Vetra, Peebee, Jaal, Samara, Thane, etc.
2. Connor Kenway (Assassin's Creed 3). I could've chosen any of the Assassins from other games - Ezio, Altair, Edward Kenway, Bayek, Aya, or Kassandra - but something about Connor simply spoke to me. He's mixed-race (part Native American, part Caucasian) in a time where he would've been looked down upon for being whom he is. His mother was killed early in his life by people he thought to be Templars. But he simply looks for the good in everyone, is one of the nicest characters in this series, even tries to make peace with the Brotherhood's sworn enemies, knowing all the good it could do. His fate particularly sucks because he loses everyone he ever cared about for a cause that isn't even his. But I have to say that the way he keeps getting back up after getting knocked down, his determination, his unfailing kindness...we could all try our best to be like Connor.
3. Silver (Pokemon Gold/Silver/Crystal/HeartGold/SoulSilver). This is a controversial decision, I admit. I could've gone with most of the evil team leaders (Giovanni, Guzma, N, and Colress being the main ones), some of the rivals (Gary, Cheren, Bianca, Hau, Gladion, Hop, etc.), even some of the leaders/Elite Four/Champions. But Silver arguably had the most growth out of any character in the series. He starts out as a petty thief, stealing the starter who's stronger than yours. He basically continues to act like an abusive asshole towards his Pokemon, is a constant dick to you, and refuses to admit he's less skilled in battle than others are. But he at least has a good excuse for being that way: Giovanni basically abandoned him as a kid for the sake of Team Rocket, and Silver wants to prove that he can never be weak again. But eventually, he starts to care more about his Pokemon, and slowly begins to understand what he lacks. He grows from a evil prick to someone who - while he'll never be your friend - at least becomes somewhat of a good person.
Honorable mentions (that aren't from the series I mentioned): Talion (Shadow of Mordor/Shadow of War), Zevran (Dragon Age: Origins), Fenris (Dragon Age 2).