The Matrix will not win any of the important awards, most likely not even nominations in categories like screenplay or direction, but it will probably win some technical ones like FX or Sound or something of that nature. The strength of The Matrix Reloaded and Revolutions will be their revolutionary techniques to present a scene, but not the actual scenes. They are ground-breaking in terms of what we can put in a movie, but they are not in and of themselves ground-breaking movies. They are simply fun and entertaining movies with a little philosophy thrown in. However, fun and entertaining got Chicago an Oscar last year, so I may be wrong.
Peter Jackson has a shot at best director, but it is not in the bag as the academy has never consistently liked films that deviate very far from our actual world, even though LOTR will probably go down in history as a symbol of cinema in this decade. He will have to contend with directors of films that are more Oscar friendly, like perhaps Gary Ross for "Seabiscuit," Joel Coen for "Intolerable Cruelty," Edward Zwick for "The Last Samurai," Mike Newell for "Mona Lisa Smile," Lars Von Trier for "Dogville," and Anthony Minghella for "Cold Mountain."
Just be glad this isn't the RottenTomatoes forum, or you'd be insulted to death for even suggesting the Wachowskis as Best Directors.