What Darwin Never Knew" explores the mechanisms of evolution at the level of embryonic development, a field now called evolutionary developmental biology (or evo devo). It is based largely on two books by biologist Sean Carroll, including The Making of the Fittest which I read and discussed here in 2008 (I called that post "Evolution: Under the Hood"). Carroll himself is one of a number of researchers who are interviewed about their research in this episode of Nova.
Charles Darwin was an amazing scientist - his explanations of the power of natural selection to produce "endless forms most beautiful" has truly stood the test of time. But there was a lot that Darwin couldn't know that scientists can and do know know now, thanks to their ability to read and interpret the genetic code. Of course "interpret" is the tough part, since just knowing the sequence of DNA (e.g. the remarkably similar genomes of humans, chimps, fruit flies, etc.) is just the first step. It's a great detective story involving genes that activate other genes that in turn control still other genes. Scientists have not only found intermediate fossil forms such as a fish with leg-like front fins, they have figured out how the genetic control methods work to make huge changes in function (fins, hands, wings, etc.) from relatively small changes in the DNA.Great stuff!
Update: Embryos of fish, dogs, and other creatures are amazingly similar. See if you can tell what's what in this interactive quiz.