Here's what I wrote about Encounters At the End of the World more than a month ago:
Having seen Encounters at the End of the World it doesn't strike me as Academy fodder. Yes there was an outcry when Grizzly Man failed to get nominated, but unlike the recent outcry at the 4 Months, 3 Weeks, 2 Days snub which was actually commented upon within the Academy, there was no indication that the documentary nominating branch felt any remorse over leaving it out. Herzog is a controversial figure, especially within doc. circles. Plus Encounters at the End of the World doesn't have the focus or the heft, not to mention the box-office or critical acclaim, of Grizzly Man so it seems like an unlikely make-up. Finally, Herzog takes aim at a previous Academy-sanctioned documentary, March of the Penguins, lashing out at it several times in the film. It's beautiful, but if there's a slot for a film with uncertain political relevance in the lineup, I'm betting it'll be the critically-beloved Man on Wire or something as yet unseen.
I will add: the film is great if you're a Herzog fan (though perhaps if you're TOO much of a fan it'll pale in comparison to his best docs like La Soufriere and Land of Silence and Darkness). In a way it's more about him than it is about Antarctica and its part-time residents. Scientists are likely to be positive on the film, though. I have a friend who researches the same kinds of organisms that a group of scuba-divers in the film study (only he gets to do it in warmer waters- the South Seas, usually), and he loved the film. On the other hand, I've been priming him with Herzog DVDs for the last few years too...
Man on Wire seems hard to beat, in my opinion. Very high production values, terrific emotional arc, and more topical relevance than you might expect going in. But I haven't yet seen Trouble the Water or most of the other possibilities yet. I have seen Nerakhoon: the Betrayal, and must admit it doesn't seem like a likely nominee- which is too bad, as it's a terrific film, but it has some arty flourishes that make me wary of its chances. I'd love to be surprised by a nomination for it.
I'm not surprised American Teen was left out- too much like reality TV and too little like journalism or cinema. Sundance buzz on Fuel was pretty weak, so I skipped it, but that doesn't mean the Academy might not like it better.