Short story, use SUPER. Easiest to use, and still providing very high quality (though not as tinkerable with as the more specialized authoring apps).
MediaCoder isnt bad either, but the convenience of SUPER and its integrating of various separate apps in an easy to use package makes it the more recommended one.
If you want the very best quality (unnoticeable to the eye, then Pegasys has a commercial hughgrade mpg2 encoder for around 69 $, if I remember correctly)
Needless to precise, these are withing the reach of normal users (SUPER is a bit useless to more advanced groups, as they play directly with every part of the encoding chain, for the very nicest looking encodes).