what are your ffmpeg issues, i compile this alot, make sure to get the latest SVN build.. also encoding mplayer which comes with mencoder (encoding part) and I I remember correctly, your can configure mplayer with the --disable-mplayer which then only compiles mencoder, their is also vlc which can be used.. but really depends on what your doing.
you can find my compile flags on
http://mvstreaming.com/set-up/