I'm producing a product that involves a composition of several videos, over alpha layers, and there are surprisingly few options aside from image lists. Quicktime's RLE (Run-Length Encoding) codec allows for an alpha channel, but was designed for animation—the encoding is over single rows and relies on swaths of consistent color, which does not apply to my current video and results in an exorbitantly large file size, making it difficult or impossible to play back in real time on my machine.
Surely there are recommended and hopefully open formats which allow for alpha channels, but have a more reasonable compression scheme. Unfortunately I'm not sure what they are.
Is there a codec recommended for high-color-variation videos with alpha, which provides a workable size?