Quicktime has always been a hassle for me. With all of the frame offsets, gamma issues, colorshifts and the corresponding agony it was generally pretty painful. It did have some features that made it the container of choice. Now Apple is partly retiring it and it will most likely be phased out and finally someone is up to replace it with a decent container format. And that would be Brendan Bolles (who under the name of fnordware release the famous ProEXR plugin for AfterEffects which is now open source).
Introducing MOX. Please support it if you can!
P.S. Yes i am aware that for now it is only replacing the intermediate format part of quicktime, not so much the delivery part. But hey, it’s a start