Footage of President Bill Clinton in the first few minutes of the film is not related to an official apology by the US Government for MK ULTRA experiments, rather for a similar project: The Tuskegee Experiments. The Tuskegee syphilis experiment was an infamous clinical study conducted between 1932 and 1972 by the U.S. Public Health Service to study the natural progression of untreated syphilis in rural African-American men in Alabama. The experiment's subjects were told that they were receiving free health care from the U.S. government.
Thomas Blackburn is an homage to Hunter S. Thompson. With his drug usage, political ties, love of guns, and outlaw lifestyle--he is a clear representation of Thompson's "Raoul Duke" persona.
Christopher Nolan was at one point attached to direct, but chose instead to work on interstellar.
At around the 50 minute mark, Thomas Blackburn (Ted Levine) mentions a story by H.P. Lovecraft about a scientist using radio waves to be able to see creatures from another dimension in his own dimension. The story he is referring to is "From Beyond", written in 1920 and published in 1934 in "The Fantasy Fan" magazine.
The original script was intended to be a first draft for Uwe Boll's adaptation of Alone in the Dark.