You know, this thread started as a serious question on the way games present morals. There really aren't enough big-selling games out there that will make you think long and hard, because anything risky or controversial doesn't get a green light. It's too much of an investment to gamble with. Haze, a shitty game that none of you have probably played, tried to make a point about drugs and/or war and/or something but as I said, it's pretty shitty and it failed to do so. If you want to play something with a purpose, a theme, a message, you have to look into independent games. That's really the only place you can find what we're looking for without hours and hours of gameplay padding. I've even played a few Flash games that had me thinking over their content long after I finished them.
But of course I can't remember any. Hopefully I will before this thread dies.