Ok, heres a workflow that doesn't work. I shot some footage in Agra India of the Taj Mahal for a travel story. I shot flatter less saturated footage using lower contrast and saturation in the Neutral Picture Style. I converted to Pro-Res with MPEG Streamclip and put together a few clips in After Effects.
Three adjustment layers later the footage is completely unusable. Every type of artifacting and aliasing imaginable. There are clips where three parts of the images are banding and jumping at the same time.
Not surprising considering that what H264 video is essentially a series of pumped up Low Res JPEGS. (http://prolost.com/blog/2009/12/3/you-didnt-believe-me.html)
What I've learned:
Shoot it right to begin with. Forget shooting flat. You get one grade in post on this thing, make that count.
Use compressor to take your footage to Pro Res. It takes forever, and there's a reason for that. It's doing a better job.
Shadows accumulate noise. There's no way you can grade your shadows upward without creating a jaggedly mess. Shoot a stop over and take your highlights down instead.
Lastly, the 5d is amazing. I love using it. You just really need to be careful of the camera's limits, because they are very very unforgiving.