Best Plot: The entire Metal Gear series (with the exception of Snake's Revenge of course), since they're all interconnected on a fundamental level.
Worst plot: Halo and Advent Rising, Yadda yadda, evil aliens, yadda yadda, destroy mankind, yadda yadda, secret weapon, blah blah, only one man can save the day, yadda yadda, ditto, ditto, etc., etc.
Initiate discovery! Fire the Machines! Throw the switch Igor! THROW THE F***ING SWITCH!
The best plot? I can't decide which game I've played had the absolute best, but both of the KOTOR games were pretty in-depth and kept me interested for multiple play-thoughs.
But deciding on the worst of those I've played is easy: Ninja Gaiden. I'm sure that it started as a good idea, but nothing is ever explained in enough detail to you, so you have no idea why your at a certain place or trying to find someone. Not to mention that the plot is full of holes. An hour into the game, the character dies, yet he's up again the next day.