In searching for a provider for this, I did extensive testing with the key companies in this arena -- Encoding.com, Zencoder, Ankoder, and Heywatch.
I found Heywatch and Ankoder to be less than recommendable. Encoding.com was my first choice (as a hunch) to begin the search, and their service performed very well and their documentation was adequate.
Zencoder was the clear winner for me and is what we decided to go with. They have exceptional documentation and a clean API. They deal with issues fast whenever their is an problem that occurs. I would recommend them for anyone who is looking for transcoding, and since they are now a part of Brightcove ($$), I only see the service getting stronger.
Note: I am not affiliated with any of these companies and think my response is relatively unbiased.
