"...Brandon Cory suggests that exporting a Quicktime reference movie from Final Cut Pro in the Animation codec and then running that through Compressor’s H.264 encoder should retain the proper gamma settings...Apparently using the right codec, one that doesn’t mess with gamma on export, is still a key to successful H.264 encoding.
david@kosmos pointed out ...the easiest way to make an H.264 Flash file from an H.264 Quicktime file is to change the extension from “.mov” to “.f4v”. That’s it. On the Mac I had to go into the H.264-encoded file’s “Get Info” properties and change the “Open with” attribute to Adobe Media Player..."
Update: The QuickTime Gamma Bug, posted on December 31, 2010 at vitrolite, is a thoughtful and deltailed an any article I've seen