While this is not always optimal, in practice most of the common cases are.

  ffmpeg -i big_buck_bunny_1080p_h264.mov -ss 45 -vf scale=320:160 -gifflags -transdiff -frames:v 50 -y bbb-notrans.gif
  ffmpeg -i big_buck_bunny_1080p_h264.mov -ss 45 -vf scale=320:160 -gifflags +transdiff -frames:v 50 -y bbb-trans.gif

  -rw-r--r-- 1 ubitux ubitux 1.1M Apr 19 19:00 bbb-notrans.gif
  -rw-r--r-- 1 ubitux ubitux 378K Apr 19 19:00 bbb-trans.gif