yes, I've seen Aguirre and loved it. There are things that seem lifted directly, and things that harken to the tone of Herzog's film. Two things I can directly correlate would be the statement made by the main character of each film by 1) in Aquirre - blowing up the raft of dead soldiers that were to be buried and 2) in Apocalypse Now - Willard shooting the dying Viet Cong civilian after the crew have opened fire on them because of the puppy. Both are very powerful statements of the main character keeping the mission on track... dipping into each's own mania.

Great stuff.