Sorry, no links. The reason: no one knows what you're trying to do. Sometimes AE would be the right tool for the job, sometimes AME would be.
It's like asking, "Which is better, a ball peen hammer or a claw hammer?"
The Adobe Media Encoder has more options and templates for working with just about everything. The After Effects render queue is really just for working with video files. However, I don't use the AE render queue unless I have to. Now that I'm not on CS6 I don't use it anymore, but if you still work on CS5, a friend of gave me a fantastic droplet called AERenderQ, that allows you to render your comps in the background so you can work in other apps while it's rendering. Here's a link...
This is a great thing if you wanted to render out some AE comps while you were working in another editing software like Premiere Pro or FCP.
Another important difference between the AE render queue and AME as I just read on an Andrew Yoole post.
As the other guys have said, don't use AE to render using temporal codecs. Temporal codecs like H264 rely on storing partial frames based on earlier information. AE renders and encodes one frame at a time, so most of the efficiency of a codec like H264 is lost. The result is that you get much lower overall quality from an AE h.264 render than if you were to encode it externally.
Adobe Media Encoder or Quicktime 7 will encode great quality H.264 files