Technically, Werner Herzog's Aguirre: The Wrath of God doesn't have an official soundtrack. The entire score was recorded by the German progressive band Popol Vuh (the first of many collaborations they did with Herzog), and was released as an album in 1975, with a 2004 re-release. Only two tracks were actually used in the film: Aguirre I and Aguirre II. If you disdain the rest of their Krautrock, the magic of iTunes and Amazon allows you to buy them individually. Now you can put them on a playlist, set them to repeat, and go as mad as Aguirre himself.
Hints of madness aside, Aguirre I and II are pretty incredible pieces of music and were raved about in the 1970s. I think the music is just as powerful today, even if Moog synthesizers seem to have fallen out of favor. It's hypnotic and eerie, and so very evocative of that torpid jungle journey. Never have native panpipes sounded as frantic and terrified. I've embedded Aguirre I below the jump, but I highly recommend spending the $0.99 so you can download it to something hand-held and listen to it in the dark.