Civ4? Any Paradox strategy game, especially Hearts of Iron 2 and Victoria 2? Diablo 2? As many people said, New Vegas?
If you're going to put some of these random indie-aesthetic games, how about their actual inspirations, like Yume Nikki or Cave Story?
Persona 4 should be up there too. I would honestly vote that game as having the best story and characters of any game I've ever played. Yeah, it's Japanese high school, whatever. The characters are fucking real, the aesthetic and style pulse through every single scene and the entire interface, the motivations and behavior of everyone involved is rock solid, it's incredibly funny and moving, and it actually has some serious things to say about how people form their identities. I mean, it's a game where you fight through the collective unconsciousness of humanity and every boss is a physical manifestation of the repressed sexual and social desires of the protagonists. You don't kill them, because they're an integral part of the personalities of the characters. "Defeating" them involves their being consciously accepted and integrated as part of the process of self-actualization. You know, like Jung said. You don't just kill your homosexuality, or your exhibitionism, or your nihilism; you have to stop denying them, and come to terms with them. Fucking incredible game. Persona 5 sucks though and basically destroys the entire concept by having you change other people's personalities instead of coming to terms with your own, it's a real shame. I guess I can give it points for seriously tackling a sexual assault coverup and attempted suicide and doing a decent job, but it's all downhill from there, and the characters are one-dimensional.
I am impressed with a few choices, like Tony Hawk 2 and Battlefield 1942, which are extremely good games and kind of forgotten. Katamari Damacy has a big place in my heart but I'm not sure it makes top 50. Left 4 dead and the Sims are good and should be on there. Skyrim... well, a lot of other people like it. I think it was a step back from Oblivion, which in turn was a step back from Morrowind, but I'm not going crazy about that.
Minecraft as best game, fuck off. Are you kidding me? I have more fun playing with Legos in real life.
I'm drunk on the internet, and I have opinions about video games.