Z (Costa Gavras, 1969)

For lack of documentaries on the greek military dictatorship, this dramatized account of events preceding the coup will do to fill the gap. It is set in 1963, a background in which the generals don't have absolute power yet. The judicial system however faces serious pressure to divert inconvenient crime investigations.

From http://en.wikipedia.org/wiki/Z_(film):

The film presents a thinly fictionalized account of the events surrounding the assassination of democratic Greek politician Gregoris Lambrakis in 1963. With its satirical view of Greek politics, its dark sense of humor, and its chilling ending, the film captures the sense of outrage about the military dictatorship that ruled Greece at the time of its making.