Since there's already a Ratchet & Clank and Sly Cooper film going on, a Jak & Daxter film would be cool too. Uncharted already feels like a "movie game" and (past) Metal Gears already had long enough cutscenes to make them "movie games", however, with the direction MGSV is going, I think a Metal Gear CG or animated film based on The Boss and the Cobra Unit would serve more justice than playing the game and not feeling the legendary vibes from The Boss.
Yoshi and Kirby would be great for cute films. Seriously, you have a lovable, green dinosaur in a storybook setting and a pink marshmellow with a black hole for stomach that consumes all... Nevermind, Kirby would be good for horror films.
Here's a reverse: inFAMOUS. The comic styled cutscenes in inFAMOUS 1 & 2 really did give the games a superhero and supervillain vibe to them. With an animated film like that, it would be amazing.
Metroid could make for an awesome sci-fi thriller film. Not so much of a horror sci-fi film, but something that puts you on edge, but with Samus either always being a badass and making you feel like a wimp or rarely ever flinching while still making you feel like a wimp. Come on, the games were based on Alien, hence Ridley being named after Ridley Scott, the director of the first Alien.
Deus Ex could work as a Blade Runner-esque film. F-Zero could work as a Speed Racer-esque film. Star Fox could work as a Maverick-esque film. Max Payne needs to bring more noir film love into this world.
Not a video-game to CG film, but Ni no Kuni is already a Hayao Miyazaki work. As a film, it would wonderfully, but it could destroy a lot of reasons to play the actual game. Maybe a prequel film about Shadar?
For fun: a Waluigi film. Give the creepy guy a break, how many games has he been in? Oh yeah, the Mario Party games, Mario sports games, and a Mario Dance Dance Revolution game. Compare this to Wario who actually has games and mini-game collections. Hell, even Peach has her own game and it was great, from what I heard. Y'know, by the time the Wa gets his own game - note the singular -, Toad, a Koopa, a Goomba, a Cheep-Cheep, and Torpedo Ted would have their own games - note the plural. Daisy needs her own games too. Anyway, the film could just be a comedy like many of Charlie Chaplin's films and chronicles Waluigi's misfortunes while giving a heartwarming message.