Secret Worlds: The Universe Within

From the web site: "View the Milky Way at 10 million light years from the Earth. Then move through space towards the Earth in successive orders of magnitude until you reach a tall oak tree just outside the buildings of the National High Magnetic Field Laboratory in Tallahassee, Florida. After that, begin to move from the actual size of a leaf into a microscopic world that reveals leaf cell walls, the cell nucleus, chromatin, DNA and finally, into the subatomic universe of electrons and protons."

This is a great Java-based animation that starts out millions of light year from Earth, and then zooms into quarks inside of a leaf. The whole trip takes about minute or more depending on your settings.