Considering my position as a skeptical conspiracy buff, MGS as a series has a fairly poor story overall. MGS3, on the other hand, was EXCELLENT since the story directly affected things happening to the characters rather than saying "Oh yeah, and this happened too" or "lol cheap twist", though I would prefer more backstory on each member of the Cobra unit and why they are able to throw their voice so well with their last breaths.
KOTOR is the game equivalent of Empire Strikes Back in terms of twist, execution, and all around awesomeness, AND being followed up by something good but disappointing in the former's shadow.
Earthbound (Mother 2) is a lot like the boat ride in Willy Wonka's Chocolate Factory, in that it starts off cute, quirky, and apparently innocent but gradually becomes more trippy and dark as it progresses and pulled off the whole subconscious mind journey thing before Psychonauts. Also Giygas quotes a rape scene from some movie to GREAT effect, "...it hurts,...it hurts..." "I feel... g... o... o... d...". Also also I think Pokey looks pretty snazzy in a suit