I don't watch too many documentaries, but I figure I'll share a few interesting science ones that I've seen.
Aftermath: Population Zero and Life After People
Both of these share the same premise, but were aired on two different channels (National Geographic and History, interestingly enough). Both of them are speculative looks at what would happen to Earth if humanity were to simply vanish without a trace, all at once. What's really fascinating to me is that for all the time that it's taken us to leave our mark on the environment through various types of industries, nature would virtually undo everything we did in a matter of a few centuries.
Cosmos: A Personal Voyage and Cosmos: A Spacetime Odyssey
These two are pretty popular, but I figure I'll post 'em anyway. Basically, they're sort of mile-wide, inch-deep looks at a wide variety of topics about life and the universe with an emphasis on making them more accessible to the general population, keeping the actual math and science relatively simple and focusing more on what it all means. Both of them were put together by some of the most brilliant minds of their times - Carl Sagan for the original, and Neil deGrasse Tyson for the more recent, modern rendition. Regardless, they're both great shows if you have even a passing interest in astronomy and the science of the universe.
Prophets of Science Fiction
This one is a series that examines the written works of science fiction authors, such as Mary Shelley and Isaac Asimov, and shows how many of the things that they wrote about as fiction wound up becoming reality when technology caught up to them. It's not the greatest show (some of the links between author and technology are sort of tenuous), but it's still a neat show if you're into sci-fi.