The Wellcome Trust have excellent short animation clips on a variety of topics.
There are animations about:
Tuberculosis - how the human immune system attempts to contain a tuberculosis infection, and how the bacteria are transmitted to new people.
Lifecycle of HIV - How the human immunodeficiency virus (HIV) replicates inside white blood cells integrates with human DNA, and produces new viruses.
DNA Sequencing and the Malaria Life cycle.