I am expecting a lot of Disco Elysium, here...and nothing wrong with that!
A video gaming student organization I was once part of actually had a vote on their favorite sayings. The winner was the evergreen "Perhaps the same said could be said of all religions..." from Castlevania: Symphony of the Night! https://www.youtube.com/watch?v=OMTizJemHO8
My personal favorite? It's hard to say...but hey, that's what the scientist in Half-Life can comment, word to word! So maybe I'll put forward, said by the aforementioned: "My god, what are doing!?"
When I first played it as a youngin, I thought the Gravemind cutscene from Halo 2 was the deepest shit ever and had every atheist cell in my body vibrating at the speed of light
"This one is machine and nerve, and has its mind concluded... this one is but flesh and faith, and is the more deluded"
"Lies for the weak, beacons for the deluded"
Green cyborg man and eldritch horror own the alien paladin by proving that his religion is fake with facts and logic