AM (the god-like supercomputer from I have no mouth, and I must scream) vs. the Matrix (from... well... the Matrix).
Both being the same thing in some ways (megalomaniac computer systems which have developed intelligence and self-conscience) the fight would be interesting because the Matrix would be the "good" side of this pair in comparison. Didn't think that would happen some day soon... Also, since both have total control over almost every aspect of reality in their respective fictional context, this would be one hell of a battle. Can you say collateral damage?