I haven't featured any documentaries on this list so far, but I think Ben Stein's courage to be one of the few (secular) voices of truth, butting the media and mainstream description of Intelligent Design, deserves an exception.
Even the title of the documentary alone, "Expelled - No Intelligence Allowed!" is a stroke of genius in itself, because by refusing to recognize the existence of intelligent information within the very basest form of life, namely within every living cell, and by refusing to acknowledge the fact that there can be no form of intelligent information without an Author, thus leaving the Evolutionary theory flawed at best, if not totally insufficient to explain where we came from, and thus crying desperately for a more sensible answer, the so-called "science" lobby Stein addresses in the movie prevents intelligent thought from happening altogether within their institutions.
Equaling their bias to practices of both the 3rd Reich as well as formerly Communist East Germany (both nations heavily influenced by the teachings of evolution) couldn't be more appropriate.
Apparently Ben is beginning to pay the consequences for his boldness, like any other lonely voice for the truth, but history will tell who were the blind, misled masses and who were the heroes that dared to speak up for the truth when nobody else did it...