Will, I prefer Squeeze as it is independent of many of the format wars that go on with video and audio compression, as they include most every format. Also, very very easy to use. Might be worth a download and trial.
http://www.sorensonmedia.com/video-encoding/
Compressor is very good if you are formatting for HTML5 and other newer web technologies. It is an extremely easy to use product as well.
If you find yourself in need of many different audio and video formats, Squeeze is the way to go.
Take care,
Jonathan