Heh everyone's wrong the smartest game ever was Earthbound, so many hidden little things in the text it's funny for everyone (ok ok yes I'm being a Earthbound fanboy =( sorry) The design for Chrono Trigger is obviously smart and a great branching story to go along with it. I'm currently downloading Portal but so far it looks very smart. A lot of the PC games are smart, either in gameplay (starcraft), or story (half-life), or just awesome (many point and click adventure games on PC).
One last one that hasn't been mentioned ZACK AND WIKI (BUY IT!) The puzzles are very smart at times.
MaxwellGT2000 - "Does the amount of times you beat it count towards how hardcore you are?"
Wii Friend Code - 5882 9717 7391 0918 (PM me if you add me), PSN - MaxwellGT2000, XBL - BlkKniteCecil, MaxwellGT2000
