One very interesting codec is Dirac, which was made by the BBC. It supports lossy and lossless compression, 16-bit even. It uses wavelets like JPEG 2000, so it also appears to do the auto-proxy thing you can do with JPEG 2000.
I plan to add some other codecs as well, such as PNG and OpenEXR, so you'll be able to render linear float to a movie format.
But the key is that this is an open movie format and I'm releasing the plug-ins as open source. You can already see the code for the WebM and Theora plug-ins on GitHub. So you will not have the Microcosm problem, or even the problem with QuickTime being a closed format. It will be completely open for people to port to any platform.
Now, I still have a lot of work to do on this project! But for now you can try out the Theora and WebM plug-ins and give me feedback (you'll have to render your AE project through Media Encoder).
BTW, WebM's new codec, VP9, should be adding some features that may be useful to us, like alpha channel support and maybe even lossless/10-bit.
It has always bothered me that people were storing their pixels in proprietary formats. I've made plug-ins for a variety of still image formats, and now I'm going after movies. Stay tuned.