I'd have to say Chrono Trigger made me feel really intelligent, it had a pretty basic throw this in your face type of stuff, but with all the time traveling, general attitudes that people displayed when you'd change the course of events, and some of the games underlying tones were absolutely amazing when you figured them out on your own. For an SNES game I'll give it some Kudos :P
I'll also vouch for MGS3, alot of what I did in that game came back to kinda slap you in the face, it really made me think alot of what I was doing to be right or wrong, then the ending kinda slammed a bunch of what you already thought into proper context, you reasoned with a lot of the actions in that game, and for that I came out of it with a pretty thought out experience.
From 0 to KICKASS in .stupid seconds.
