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.

goof troop

If you're looking for what I think you are, why is Fallout 2 on the list?  It had some nice writing in places, but the actual overaching story was pretty bland.

I can't think of any game that has really struck me as "smart" or that has had a really intelligent story.  Honestly, I prefer games that toss out all that BS.  Skies of Arcadia made me happy because the story was simple, effective, moved the game quickly, and came almost baggage/emo free (almost impossible to find a JRPG like that).

Pretty much anything by Bioware outside of Neverwinter Nights could probably get an honorable mention but all had their flaws.   I liked Baldur's Gate 2 simply because the main villain was interesting as a character... up until they explained his motivation that is.  Jade Empire was good overall, but everything felt half done.  Concepts felt half-finished everywhere.  It was like they had all these great ideas and started putting them into place then decided to just not flesh them out.

I've passed the point where garbage seems amazing (FF7) and I'm now to the point where I really have no high expectations from video game stories.  If they can stay interesting and not bore me, that's more than I expect from the get-go.

^hey, garbage is fun.

Smart ... well none is thats mart actually . Yes MGS games have a good plot , so does GoW , but Im actually looking for nice stories , stories that are not complex but still can translate their thaughts better via feelings . Thats why I liked games like ICO , Prince of Persia SOT trilogy , SoTC , God of War and yes , to some extent even some of the FF games . IMO this is the reason why 7 remained such a popular game even to this day ...

^yeah, God of War...best plot for an action franchise in ages.

I'm not basing it on story-only. Looking at my OP, I didn't properly clarify that. I think Fallout was smart, not because of the writing, but because of some of the characters and the complete freedom allowed by the game. Wanna be a hooker? Go for it. Watch out for those STDs, though. Wanna kill little kids? Go for it, but beware the death squads.

It wasn't the story that sold me on Fallout 2, it was everything else. But, you already know that, being a Fallout fan and all.

BTW, I agree about Bioware. They always seem to do just enough to make the story interesting while not going overboard and making it confusing for confusion's sake. But, like you said, they never seem to go that extra mile to push the game over the top.

Shadow of the Collossus. Another excellent example of a smart game.

Final Fantasy VI

And no, I'm not listing this just because it's a FF game. The game actually had pretty complex characters that just about all of them were very well developed. The game also dealt with pretty difficult love issues, genocide, and even suicide.

How rare is a smart game that demands you to be smart?

Examples , anyone? I think I already mentioned a couple. Maniac Mansion, King Quest, and to some extent Dragon Quest 4