Science, History, etc... there are lots of great documentaries on all of them.
So, suggest some.
I'll go first, Sex in the Stone Age by National Geographic
About the sequencing of the Neanderthal and Denisova genomes.
http://www.youtube.com/watch?v=c678VIdEDdg
Connections. All of them.
http://en.wikipedia.org/wiki/Connections_(TV_series) (http://en.wikipedia.org/wiki/Connections_(TV_series))
http://youtu.be/WgOp-nz3lHg (http://youtu.be/WgOp-nz3lHg)
Old but gold, someone has put all of the early Michael Wood 'Dark Age' documentaries on youtube.
This one starts in a Malmesbury Abbey about 45 miles from here.
http://www.youtube.com/watch?v=GCsXLdytwj8 (http://www.youtube.com/watch?v=GCsXLdytwj8)
That uses Stephminx appears to be the best bet for seeing all of them.
Anything by Michael Moore.
I asked my favorite paleoanthropologist a question inspired by that documentary and he answered within the hour! :w00t:
http://johnhawks.net/weblog/mailbag/denisova-diversity-2012.html
Dogs Decoded, a NOVA documentary on the domestication of the canine, their evolution with man, and how recent research over the last 30 years in canine intelligence shows how they actually outscore primates in certain cognitive intelligence tests.
My favorite is a very strange one called Fast, Cheap and Out of Control (and no, it was not about co-eds. :P):
http://www.imdb.com/title/tt0119107/
Battles B.C.
Not online, I think. It's about famous battles of the antiquity, notably the Jewish exodus from Egypt and the conquest of the land by expelling the native. It tells of the myths, and how they relate to what most likely happenned given what we know. They also have a few on Romans and Alexander the Great. It's done in the 300 style.
There was a series on History about myths, explaining the myth itself (could be Hercules or Thor), and also examining (in less detail, unfortunately) the origins of the myths and how they may have come about. It was hit and miss, but not too bad.
Has anyone recommended the documentary on Stalin's ape-man army? If not, then that one.
2016: Obama's America.
Food Inc.
http://topdocumentaryfilms.com/food-inc/
The Corporation
http://www.thecorporation.com/
It felt topical. :P
Kurt Sutters Outlaw Empires (are on youtube)
Here is a link to a site that hosts some documentaries for free and links to other sites where they're available as well: http://topdocumentaryfilms.com/