Games that make you think

As the gaming industry has evolved, so have the ideas behind games. We are more frequently getting games that are much more then mindless, and personally, I like the trend. I'm talking about games like Bioshock, of course. Beyond that, though, games with interesting stories that make you want to further study their lore, or that force you to consider alternate perspectives. I love these kind of games, Eternal Darkness, Bioshock...

Anyways, I just wanted to know what everyone thinks about all this, and what your favorite games are that have been making you think. I'd like to discuss this, as well as discover some of these I may have missed.

Portal is definitely one of them.

Yeah BioShock did make you think about what you should do to get through the level; like thawing ice to continue through a sealed door. All games have a certain thinking level.

Also the type of games that allow you to use the environment insted of pumping the enemies with lead.

Mass Effect: One of the few Sci-Fi games (or games in general) to take an interesting look at the human race. Rather than just being the good guys, ME not only looks at the weaknesses of mankind, but also our strengths.

The Witcher: One of the best examples of "gray area" decision making. Rather than choosing the good option or bad option, you're choosing between the lesser of two evils, and the "lesser" is pretty subjective.

Portal: A great game that proves a unique setting and gameplay are more important than length, graphics, or attaching chainsaws to guns.

Ninjabread Man: Makes you wonder how awesome that game would have been if a good developer were behind it.

Big Rigs: Makes you question your faith in humanity.

Definitely Planescape Torment.....not only is the entire game an examination of identity, but the conversations throughout the game provide stories that make the player think about things such as War, Religion, Love, Hate, Greed, etc.....and it examined these subjects without being preachy and instead through simple story.
Just one example of one of the many many amazing experiences and conversations in this game that show what an intelligent game it is happens when the player is using one of the sensory stones as is getting a memory of a 2nd-in-command military officer on a battleship bombarding a civilization below and he asks the capatin how they will ever be able to live with themselves with all the civilians they are exterminating, and the commander replies that the only way he can stay sane and carry on his duty is to believe what his government has told him, even though he knows it's not true...which is to pretend that there are no civilians down there, just enemy soldiers and bases and that in war, the term "enemy" is something that can and does get used broadly. Of course the way the whole story is worded is a million times better then the summary I gave.

BioShock is another game that makes you think. It makes the player really question "Why am I doing this" in which no other game has ever done in the twist answer that it provides. Most games provide a lame story as to why the player character would blindly go blasting away at a million enemies and do things as the game instructs them to do......BioShock adds a new dynamic in showing that not only is the character not in control, but neither was the player....and all the time they didn't know it.

Deus Ex and Beyond Good & Evil both examined government corruption, lies, and false propoganda put out by those who want to stay in power by controlling the masses through false information....and that it isn't always wise to blindly accept what those who have power tell you to be true cause the opposite can be true.