This one is easy for me: the latter half of the rescue scene. The bit where they are in the chopper and Neo is opening up the mini. The lobby shooting spree is a close second but it simply has too many errors.
The enitre film is classic. Every frame done perfectly. If I had to choose one sequence though, it would have to be the lobby shootout. As much as I like the martial arts aspect of the Matrix, you can't beat a good old fashioned shoot up. A shoot up done so stylishly.