The sites listed below are collections of short animations (not full-length videos) that demonstrate Earth processes and formation.
SERC has the largest collection of visualizations on geoscience topics (over 100!).
Animations corresponding with the introductory-geology textbooks Earth: Portrait of a Planet and Understanding Earth. For Physical Geology, you will have to search for videos by selecting each chapter from the pull-down menu first.
IRIS has quality earthquake animations.
MIT has created a collection of Visual Earth animations showing geologic processes such as the fluvial environment, glacial structures, normal faulting, graben, and graben and horst series.
Geology animations (in Flash) from the University of Kentucky.