I've tried a few different things with PLY files and no luck. Actually, I'm not 100% sure if Blender really likes PLY files anyway - you can't even export color easily in PLY format in Blender. So, I've given up on PLY and have hacked together a bit of a messy OBJ exporter: http://paste.yt-project.org/show/3205/
I'm probably doing the colors wrong, since there's likely a nicer way to get actual "face" values then just taking the value at 1/3 of the vertex values, but it worked, so I didn't mess with it too much.
A few other things: (1) in theory, this can set transparencies, but I haven't got that working as of yet, (2) the default specular (ambient?) color settings make for a bit of a washed-out view in sketchfab: http://skfb.ly/54jged0b, (3) the .mtl file is a bit too long since I'm essentially setting each face as a different material, when one would just like to use 1 material per color and set all the faces with that color on a specific surface plot to that material, but I haven't got that bit working well either.
Thanks for the info, and please let me know if any of that doesn't make sense. -Jill