A few weeks ago I posted a link to a cicada lifecycle video that won an AAAS multimedia award. I just spent some time browsing around the other submissions, and was pleasantly surprised at how much other good material was submitted.
Transpiration: Water Movement Through Plants (a flash animation) is an honorable mention in the interactive category; it walks the user through the effects of changes in various elements (temperature, cuticle thickness, etc.) on rates of plant transpiration. Even more interesting, though, is that the animation provides details on root, shoot, and leaf transport of water that are useful for introducing the basics of those processes (the root animation is the most detailed of the three).
The Synapse Revealed (medium image) is a beautiful drawing of a synapse that won the illustration category's top prize.
The Essence of Fluorescence (large image) is the winner of the information graphics category; it provides an elegant pictorial reference for the many fluorescent dyes available.
[Update Nov. 14: Added new links - the original links were all based on the 2005 Visualization Challenge slide show (dead link), which the AAAS has apparently removed from its site. The original, currently dead, links were: 1, 2, 3, 4, 5, 6, 7]