Regarding "The Prisoner" that you mentioned earlier, I just read a review of the game. I found it interesting that the concepts they explored in the game (freedom and independent thinking) are under attack in today's world. They didn't mention anything about philosophy in the review, but that doesn't mean it doesn't come up in the game at some point. There was also a sequel to this game: "The Prisoner 2".

Two additions. Was going to mention Planescape Torment as well (What can change the Nature of a Man?), but it has been named at least twice already.

Knights of the Old Republic 2. Especially Kreia's interpretation of The Meaning of The Force.

Well. If only because of the proper story in the movies, Blade Runner could be added to the list.

Also I have not mouth and I must Scream

I never knew there were games! But as for the show...

"I am not a number... I am a free man!" ;)

There are so many. Can you narrow it down a little?

https://en.wikipedia.org/wiki/List_of_philosophical_concepts

Torment: Tides of Numenera

It hasn't been acclaimed as its predecessor (Planescape: Torment), but I'd recommend it !

The Legacy of Kain series of games explore the concept of free will quite a lot and weave an interesting story around it. Not on the level of Frank Herbert's Dune mind you, but if you like your vampires with philosophy and shakespearian dialogue, you won't be disappointed.

Seconded.

Also seconding someone's earlier mention of I Have No Mouth and I Must Scream, by far my top pick.

Very glad to have both here DRM-free on GOG.

Arcanum and Legacy of Kain series have quite thought-provoking takes on topics of religion and prophecies.

No One Lives Forever features some interesting discussions on correlation, causality, social determinism and personal responsibility. If you listen to the henchmen's idle chats instead of shooting them immediately.

And the Blackwell series is what ghost stories should be in terms of reflections on life, death and regrets.

Guns gore and cannoli is, on the other hand, a bit light on philosophical content. I noticed.

Jolee struck me as more philosophical in the first KotOR.

While I agree that Jolee is more "philosophical" than most other Jedi in the sense that he is the first that I remember being presented as more than (or even a combination of) good or evil, Kreia constructs a plausible, rational arguement that The Force itself is evil and should be destroyed for the greater good.

But, reasonable people can disagree.