I asked my friend Jamie Doornbos to make a list of the cleverest computer / video games from the perspective of someone who is a programmer rather than a player. Jamie was the lead programmer on The Sims, the best selling game ever, so I presume he knows his stuff... Jamie says, "These are my Top Ten Games From a Programmer's Perspective (in no particular order). Surprisingly enough, I don't actually get around to playing a lot of games."
Sim City 2000 There were some really nice tile-based algorithms in this.
Parappa the Rappa Nice paper doll graphics and rhythm engine.
Mario 64 One of the first games to attempt a fully automatic 3D camera, and did
a pretty good job too.
The Sims Data driven object system, enabling lots of plug-ins.
Wolfenstein 3D First corridor renderer.
Roller Coaster Tycoon 2 Cool tile-based coaster construction kit and very believable simulation.
Eye Toy Groove Camera integration and motion detection.
Grand Theft Auto 3 Excellent all-around game engine, including missions and localized world population.
Ico Amazing inverse kinematics for the hand holding.
Rome Total War Good group agent behaviours and flocking.