I've found a way that works for me at least. It's the single most annoying thing about quicktime. I've spent years dealing with that crap LoL. I've done all of the above - many times in many different ways (even many variations of x264) and nothing works reliably. Problem is you don't know if your clients are using QT7, 10 - or whatever - and having them change their QT is also an unknown variable I'd rather not deal with.
But with way too much trial and error I've discovered something that works, at last - at least for me in my current setup. And it's so simple:
In AE project settings, enable color management, set as sRGB, and check the checkbox for match legacy.
Bam - now you can render your QT's h264's alongside jpg sequences or whatever and they will all match between qt7, qt10, sequences etc. to about 99% - which is sooooo much better than the nasty 60% gamma/sat shift you usually experience.
I guess qt is expecting some srgb color management? I decided to try it after reading Ken Rockwell's article on photography color management (
http://www.kenrockwell.com/tech/color-management/is-for-wimps.htm) and how just making everything sRGB is a reliable way to work on stills because most everything assumes sRGB. I thought - well QT is pretty consumer-based, decided to try it for video and voila... who would have known.
Hope it works for you.
// jayse