Obviously first off, Master Chief from the "Halo" series (my username's namesake): Since Halo was my first M-rated game and first shooter (I had played purely Nintendo games until that point), he was the first badass I played in video games. His dynamic with Cortana is great, and his ability to shine as a lone hero amidst the oversaturation of brawny male FPS heroes is a testament to his timelessness. Truly one of gaming's greats.
Geralt from "The Witcher" series: This guy's amazing. I love how stoic and hilarious he can be, while also being sympathetic and a badass as needed. Definitely one of the greatest characters this medium has seen.
Bruce Wayne/Batman from the "Batman: Arkham" games: Maybe this isn't so fair because Batman has been around for a long time, but I adore Batman as a character. Such a silly concept taken so seriously makes Batman/Bruce Wayne a joy to experience. And if it wasn't already obvious, he's my favorite superhero.
Luke Triton and Herschel Layton from the "Professor Layton" series: I love their dynamic! On top of being a fantastic mystery/puzzle series, the Layton games gave us two of the most charming characters ever. They're so cute and pure-hearted, it's a joy to see them uncover mysteries throughout London and around the world. Luke is currently featured as my profile picture, though he's lookin' a bit derpy at the moment~!
Luke fon Fabre from "Tales of the Abyss": Two Lukes on this list, wow! Anyways, this is someone who nearly everyone can relate to at some point in their lives. He's a well-written character with strong character development that has to cope with a past trauma, losing friends, growing up, facing his demons, and struggle with being accepted and finding a purpose to live. He struck a chord with me.
Eva, Niel, Henry, and River from "To The Moon": I chose all four because the story of "To The Moon" is so much more powerful when viewed from the perspective of all four. Eva and Niel juxtapose young Henry and River in Henry's memories. They rewind backwards through Henry's life and the bittersweet tale of him and River, acting as a vehicle for the player to comprehend and facilitate the story, also acting as comic relief for the heavy emotion in this game. Henry and River's story is both cute and sorrowful and represent the uncertainty of life.
Noctis, Ignis, Prompto, and Gladiolus from "Final Fantasy XV": Again, I chose all four because of their incredible dynamic together. There are a lot of things to chide Final Fantasy XV for but its brilliant execution in selling the friendship and bond between its four protagonists cannot be understated. These four characters are some of the most relatable and well-executed characters I have ever seen. I felt attached to them in a way no other game has managed to do, and despite FFXV's plot shortcomings, I can look fondly at this game and its bittersweet ending thanks to these four.
Phoenix Wright and the cast of the "Ace Attorney" series: I've fallen in love with Wright and Co. for over six main entries now. Wright and his cohorts Maya, Apollo, Athena, Trucy, Edgeworth, etc. all feel special because I've got to know them over a decade of Ace Attorney games. Seeing them grow and transform, as well as learning their backstories really sets them apart from many other characters. The long run of the Ace Attorney series does definitely contribute to this.
This is all I got off the top of my head, there are probably man more I forgot. Anyways, thanks for reading!