Mo-cap would have been used to assist in creating the animation resources.

Then in-game, lots of different sub-animations are blended together along with some IK, I think.

Probably more important the raw animation data itself is how these animations blend together and transition from one to another (e.g. only transition from A to B when the right foot has hit the ground at the correct angle). We've had mo-cap in game for ages, but only recently has in-game animation (non-cut-scene) started to look really good, which, I believe, is largely due to smarter transitioning (as well as being able to store the metric crap-ton of individual animations required for something like Assassins Creed). CoD4 is another game that has fantastic animation transitions, IMO.

NaturalMotion Morpheme is some pretty nifty middleware for tackling this problem specifically.

They used Max, MotionBuilder, and HumanIK Middleware.