I usually encode broadcast level spots in QT using the Animation codec. Then, when clients need something smaller, I encode those files into WMVs or MPEG4s or whatever.
Recently, when I try to do that, the new encoded files look horrible. It's mostly a color issue. The gamma seems to have changed dramatically and (on the one I dealt with this AM) a large area of orange color was gone and replaced with black.
Here's something else. IF I encode my original content with H.264, I don't run into this problem.