Best: The Intersect
One of the coolest things about this show was its basic premise, and the Intersect was what that premise hinged on. Of course, the idea of the CIA and NSA encoding all of their secrets and intel on to a super computer able to be downloaded into the brain to create the perfect spy is utterly unbelievable. Once you get past that however, it's quite a cool concept.
Things never got stale either: Season three featured the awesome Intersect 2.0 which came complete with kung-fu, and later seasons explored the negative psychological side-effects that having a super-computer in one's brain would probably cause. Every program glitches sooner or later.