Animation of prime factorization of the integers based on Brent Yorgey's factorization diagrams, described here. [via Data Pointed, previously.]
Like most game companies, Square Enix records every significant activity that occurs in their online environments. Jim Blackhurst took a database of "terminal impact events" in Just Cause 2 and mapped each of the 11 million player deaths to to the geography of the game to create a haunting visualization.
Asteroid Discovery From 1980 - 2010: an animation of the solar system that highlights asteroids as they are discovered. I would suggest watching it in a high resolution.
Electronic Masks and Calculated Movements are two early computer animation projects featured at EVLTube, the YouTube channel for UIC's Electronic Visualization Laboratory. In additon to the video archive, the EVL website also features a trove of interesting current EV projects like snstncntnrs and Unfolding Space, not to mention extensive notes on the fascinating research conducted and devices used at the facility. [more inside]
The Inner Life of an Intelligently Designed Cell? Remember The Inner Life of a Cell animation (discussed here)? Apparently the Discovery Institute (recently discussed here) is showing it in presentations with a new title and narration, and without attribution.
The Music Animation Machine is a way to visualize complex music - fugues and sonatas and all that. Other tools, such as those mentioned previously here and here, accomplish a similar task in a way, but this is still very, very cool. Watch and download all the videos you can. Bach, Chopin, Scarlatti... if only there were more! Of course, you could buy the DVD.
Tsunami visualizations Visualizations of recent and historical tsunami episodes, collected by John McDaris at Carleton College. Includes large but visually effective animations, such as this NOAA visualization of the global propagation of the 26/12/04 tsunami (24MB Quicktime).