What are the differences between the three bundled ffmpeg prores encoders?
I found the following explanation on the ffmpeg wiki:


  Fmpeg comes with 3 different prores encodes: "prores", "prores_ks"
  (formerly named "prores_kostya") and "prores_aw" (formerly named
  "prores_anatolyi"). In our testing we've used the "prores" and the
  "prores_ks" encoders and found "prores_ks" to be the best encoder to
  use. It is the only one that supports the 4444 colorspace and although
  it may be slightly slower. The color quality of the videos produced by
  these two codecs was visually indistinguishable Because of the 4444
  support we've decided to go with Kostya's version of prores.


So, if you want to do 4444 and need alpha channel support, prores_ks is the way to go.

This blog post also suggests that prores_ks has a smaller footprint, and that prores and prores_aw are basically the same.