The series of recent posts covering the Inner Life of the Cell (see the Molecular trafficking section in Cell Biology in this forum) inspired me to look up some more sites that 'visualize' concepts in cell and molecular biology and microbiology, rather than just the pretty confocal pictures of our favorite experimental cells!
As Tony Rook points out in a follow-up comment,
"I think animation like this can really make a huge impact on both the scientific and non-scientific community. Visualization of scientific theories like this not only helps scientists better understand these concepts, but they are very beneficial to introducing complex systems to the non-scientific community. I know my family was very excited to see these and find out what the images were actually showing. As a scientist, it is fascinating for me to be able to explain to other the inner workings of cells."

Post your favorite sites and share the excitement!

CellsAlive (www.cellsalive.com)
A whole collection of images combined with flash animation covering a wide spectrum of biological processes, in multiple organisms. Sadly, the site is not fully open access, but one can view the animations on-site.