Game studies grad student here. If I'm interpreting your question correctly, you're asking about uncovering philosophical ideas in games rather than applying them. I think there's more scholarship available for the latter, and if you're interested in game scholarship in general, there are a couple great online journals I'd recommend. gamestudies.org is freely available to everyone and has articles from many of the most influential scholars in the field. Games and Culture also has some great content, although I think access to their full articles might be dependent on whether you're on a school network. A few articles that apply philosophical ideas to games (haven't read them, just using them as examples based on their abstracts): "Game Definitions: A Wittgensteinian Approach"; "Electric Empire: Orientalism Revisited in the Military Shooter"; "Gramsci and Games"; "Playing the Panopticon"

But to respond more specifically to your interest in uncovering philosophical ideas in games, I'd say few games present philosophical discussions as explicitly as Bioshock does. Here are a few games that offer a lot for philosophical discourse (but you can find ideology in anything):

• Deus Ex and the posthuman. McKenzie Wark's Gamer Theory discusses this at length and in the process draws on philosophical works.

• Spec Ops: The Line as a retelling of Heart of Darkness offers a lot to say about iperialism, military intervention, the madness of power, plus meta-criticism about the othering of military shooters.

• Kentucky Route Zero is a game I'm still wrapping my mind around, and I feel like you could excavate just about anything from it. The encounter with the unbelievable, the encroachment of fantasy at the limits of perception, stasis, simulation fever (a term Ian Bogost adapts from Derrida's archive fever) - there's just a ton there.

I'll stop there, but again we can find philosophical conversations in practically anything.