I hope that this is for playing on a portable device or a older, slower computer. Because MP4 to your typical Xvid (or Divx) AVI/WMV (non WMV9)/MPEG1 is gonna rape the video quality.
For AMV editing use (which isn't recommended--fansubs = bad), the better way would be load into VitualDub/Mod via AviSynth with DirectShowSource(). Add filters if necessary. Then output in Huffyuv, Lagarith, or Uncompressed AVI.
Having trouble playing back videos? I recommend: