Did you know that NOVA has a YouTube Channel? Well, surprise! Not all the episodes are there, but here are some of my favorites.
Cracking the Maya Code
About the decipherment of Mayan hieroglyphs. This episode includes several appearances by my former FSU professor, Kathryn Josserand (she was a linguist and Mayan language expert; there's nice remembrance of her here).
Secrets of the Parthenon
About the complexity of restoring the Parthenon in Athens. Lots of interesting detail about the science of restoration, the complexity of ancient building practices, and the destructive effects of 2500 years of war, earthquakes, looting, and misguided restoration.
Lord of the Ants (E.O. Wilson)
About ant expert Ed (or E.O.) Wilson. Lots of cool ant stuff, plus biographical info on an expert in his scientific field.
Mars: Dead or Alive
About the epic Mars Exploration Rover (Spirit and Opportunity) mission. This is a really interesting look inside NASA, with frank discussion of the risks and hardships of trying to send rovers to Mars, land them, and then control them.
Welcome to Mars
Part 2 of the "Mars: Dead or Alive" episode, produced the following year, with lots more footage from the rovers and the scientists who work on them.
More NOVA Online
The PBS Video website has 40 NOVA episodes available for viewing online, though the quality isn't quite as nice as the YouTube HD featured above. My favorite: The Incredible Journey of the Butterflies, about the transcontinental migration of monarch butterflies. It's way better in HD, but amazing even in low-resolution.