Explaining Biological Differences Between Humans and Chimps

Continuing the discussion from Uncommon or Common Descent?:

@JoeG had a great question on the science of comparative biology:

What are the mechanisms scientists have uncovered that explain the anatomical and physiological differences between humans and chimpanzees?

This is a great question, and there is just so much to cover here. It seemed like it was worth learnign about, and I wanted to pose the question here to the whole community.