Hi,
The animation codec at 100% is lossless, and supports an alpha channel. But the compression is fairly limited and so the file sizes are really big, depending on your image content.
The JPEG codecs- Photo JPEG & Motion JPEG, are practically lossless at 100% and will be about 1/3 the size of the same files compressed with animation. There will be some very minor rounding errors but no actual compression artefacts. Certainly nothing visible. However they do not support an alpha channel.
If you are totally utterly and completely anal about preserving image quality then the animation codec is your best bet. Otherwise, if you don’t need an alpha channel, Photo JPEG or Motion JPEG will save you about 3 times the disk space. In all cases, you need to have the quality set to 100%.
Personally, I use Photo JPEG at 100% whenever possible, otherwise it’s animation for anything with an alpha.
These codecs are Quicktime based and cross platform.
-Chris Zwar