This year the Academy did a better job with its short list than last year, when, arguably, the best documentary of the year (The Interrupters) wasn't even included. I would have like to see nods to Only the Young and maybe The Waiting Room or Detroipia, but we can't have everything.
Although each of the nominees would be a fine choice for the Oscar, I think this is a race between Searching for Sugar Man and 5 Broken Cameras. (The only one I haven't seen yet is The Gatekeepers, which I think is the only one that could challenge these two; it's already picked up a few best-documentary awards this year. Its release has been relatively small to date, and there's less buzz about it. It'd be hard for me to pick The Gatekeepers as the best of the year, not having seen it. Caveat complete.)
If I had a vote, I'd cast it for Sugar Man.