I saw Aguirre today. Nowhere near as good as I was expecting. For a supposedly sophisticated foreign movie, the themes were childishly black and white. More importantly (I am, after all, by this point rather immune to simplistic anti-religious, anti-American attitudes in film), the cinematography was amateurish (and yes, I am aware that that is probably the most snobbish phrase I've ever written in my life). I was expecting some beautiful nature shots, but Herzog does very little with all the lush material the forests and the river give him. A far better director, who uses similarly slow pacing, but to much greater effect thanks to the beauty of his nature shots, is Terrence Malick. Still, there were some good moments, and it was probably all worth it just for the scene of Aguirre chasing around the monkeys on his raft.
A far, far superior movie, with a similar setting, that deals with the same themes in a far more complex and accurate way (and has deeply, deeply beautiful visuals), is The Mission. Morricone's music doesn't hurt, either. So here's the trailer (try and ignore the awful voiceover dude), it's one of my all-time favorites, please check it out!
UPDATE: Speaking of Roland Joffe, who directed The Mission, this ending to his movie The Killing Fields is worth a look. Given the role hippies played in getting America to wash its hands of Vietnam and Cambodia, this could very well be the most ironic use of a song in a movie ever.