Neil Gaiman's Goliath proves that The Matrix can be fertile ground for more than just Mary Sues. It's one of the more original short stories I've seen, ever, and makes fantastic use of the universe's parameters.

I wish there were more Matrix fic out there that didn't feature Mary Sue-ish type neo-Neos, but alas, my searches have been long and fruitless. Well, mostly. Kirstma has written a fine pair of stories (Heroes for Ghosts and Zion Revisited) centered around the Trinity/Neo relationship, but what really impressed me was how well she drew the social dynamics of Zion, the last human city.