Grand Theft Auto. Whilst some other games (such as the above mentioned BioShock and Deus Ex) are good to study, I think GTA could be very good.
Why? Well, it's one of the most controversial series in the world and is developed by a company who have made a name for themselves doing so. You could study the effects on teenagers, pre-teens (like 11-12yr olds) and adults. See if it affects them, see if they change because of it. See how much you can get in a game like that - Can you get more sex into it? It's a great series to do studies on, because I suspect it's had a lot of influence on the market.
And perhaps study how the protagonist is seen by the player? Do they prefer ones like Carl Johnson and Niko who, for all their killing, are pretty "straight" guys who rarely drink and don't do drugs, or do they prefer characters who are doped up to the eyeballs? Do they like the serious characters like Niko, or the more light hearted ones like SR2's protagonist?
You could also use GTA (and games like Saints Row 2 and Crackdown) to work out what gamers like in each game and blend them together to create a better game. Imagine GTA V with a customisable, fully voiced protagonist (like SR2) but with a city the size of IV's Liberty City. Imagine GTA V with San Andreas' planes and customisable vehicles. GTA's an incredibly popular series, and I'd be very interested to see what sort of results would come from it.