One game that I can affected me on a spiritual level is actually Silent Hill: Shattered Memories for the Wii/PS2/PSP (Played it on the Wii).
*Spoilers for the game follow*
During your time in the game, you play the role of Harry Mason, who is looking for his daughter, Cheryl. In reality, this is all taking place in Cheryl's mind, as she's struggling to realize that her father has been dead for years and she's created this perfect father figure to help her deal with her loss and pain. The ending (there are multiple endings, but I came across the "Love Lost" ending) is bittersweet because she finally lets go and accepts the reality of the situation, but at the same time, she must now deal with a scar of a missing father that will never return.
This part of the story really caught my attention and affected me in a pretty big way. In the Christian Bible, God is refered to as the Father multiple times, so Cheryl's story of her searching for this perfect father figure was really intriguing. In the end, he is only a ghost in her mind, a band-aid to help the hurt of losing him all those years ago. But with the Christian world view, God is the perfect father (Matthew 5:43) who wants a relationship with us.
It's a pretty interesting juxtaposition of ideas. One showing the pain and hurt we all experience in an unperfect world, and in specific case a missing father. The other showing a Father that will never leave nor forsake us (Hebrews 13:5). It really got me thinking, and really affected me in a way I didn't think a video game could. Very cool moment. ^_^
