The best replacement for mjpeg is mpeg4.

The best alternatives to mjpeg are rated as following:
★★★★★  mpeg4
★★★★  mpeg
★★★★  h.264
★★★  dv
★★★  avchd
★  yuy2
★  rtv1
★  jpeg 2000
★  h 264
★  mpeg 2
  mpeg 4
  avchd lite
  h264
  h.264 camera
  mpeg-4
  avchd gh2

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Google Trends

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