If you have use directshow decode ticked, then SUPER will use windows media player's engine to decode the files. So unless you have the right codecs installed and registered with windows, don't use it. SUPER comes with codes to encode and decode just about any format you can throw at it.
You should use directshow decode for FRAPS movies, since fraps only registers its decoder though WMP and they're assholes and won't release an open spec for it, but whatever =|.