What is the difference between a Container and an OU in Active Directory?

An Organizational Unit (OU) is a special purpose container, that differs from a regular container in that administrators can apply group policy to an OU, which the system then pushes down to all the computers that reside in the OU. You cannot apply group policy to a container. 

In general, you design an OU hierarchy which is based on how you want to have Group Policy flow out to the domain-joined machines in your AD.