I have been using Zencoder in our product for about 2 years and have loved it. Super easy to setup through their API and I have run into very few issues over the last couple years.
However, we are running 10k minutes a month through there and cutting our monthly encoding bill in half is pretty hard to pass up. AWS definitely has less features, but the feature set they do support is exactly what we are using Zencoder for. Probably going to wait a couple months to see if Zencoder decides to lower their pricing and if not take a look at switching.