Dude, top 3 is a really difficult choice.
I'm a Herzog man through and through, every documentary he's made is beautiful and hilarious and should be watched. If I had to pick a favorite though I'd go with 'Encounters at the End of the World'. Antarctica is completely unreal, like everything you thought your brain had a grasp on (penguins, seals, ice, sponges) gets flipped around and still Herzog makes the whole damn thing about how nature makes him uncomfortable. I love that a guy who seems to really not get nature has captured some of the most amazing nature footage you will ever see.
'The Bridge' is really intense but really well done. A crew filmed the Golden Gate Bridge for a year to capture the people who attempt suicide jumping from the bridge. They follow up with the friends, families, people who have rescued jumpers and one survivor. There's one guy who's kind of a thread throughout the movie and when it gets to the end, man... I like this one because there isn't much overt bias injected, it's very quiet (see also: A Certain Kind of Death)
A more recent one that I've watched several times and am still fascinated by is 'Resurrect Dead: Mystery of Toynbee Tiles'. It's got crazy conspiracy theories, kind of renegade street art and pigeons. But not gross street pigeons, nice pigeons. Toynbee tiles are these linoleum panels that have been crushed into asphalt by cars, the tiles have conspiracy messages written in them that talk about the movie 2001 and the planet Jupiter and new broadcasters. They might even be connected to a David Mamet play. Watch it, it's on netflix instant and it is nuts! Also if you're in New York there's still a tile you can see in Soho, near the Broadway Lafayette F stop. It's on Houston, on the south east side, closer to the Hollister than the Adidas store.
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