Kerbal Space Program.
Even though I didn't go after formulas and numbers (except for Delta-V and a few other things), I got to know..What Delta-V even was!
And how the hell orbits and transfers worked. And a bunch of other stuff that gave me a more intuitive knowledge of such things, that really made it easier to learn real physics and stuff.
Europa Universalis/Civilization and similar games made me know or at least get a general idea of geographical stuff.
Assassins Creed III gave me a lot of insight in American history, given that I'm not from the US. Even though people say the game butchers history, the codex is generally written in a pretty fun and interesting way, which made me constantly go fact check and get interested. That applies to all the AC games I played, actually (up to AC4)
And in a different note, Altair from ACI actually made me think on a lot of stuff and kind of change as a person. He's one of my favorite fiction character ever, for some reason.
-- OBS: Even if Ubisoft keeps destroying the franchise for money, Altair will still be a favorite.
There are definitely way more, but I guess all of those and more have been mentioned already.
EDIT:
Oh yeah. Battlefield 2 and Battlefield 2142.
I loved to play as a commander. No commander would properly use their mic and orders/scan/supply drop correctly (at least in my view). I very rarely lost a match as commander.
I learned very quickly how to talk with very different kinds of people, and how to "persuade" them to do what you are "ordering" in a videogame.
You'd be surprised by how many people will get pissed of you for simply giving a "Take this point" order, or "Stop Spawn Camping and Defend Our Base" order. By simply changing my tone and choice of words, I'd make even the most rebellous annoying people do what they should be doing and turn over apparently unwinnable games.
My most favorite moments would be when I got to join a losing team in a random server which the commander ragequits or gets a mutiny vote passed. Then I'd rush in and save it.
Ohhh the nostalgia. It was my golden FPS days really :')