Video and audio clips are now encoded in the new embedded player, though some clips and archived content will continue to be available in the pop-up player format.
As for the video player we had to stick to MP4 format and nothing larger than the screen's resolution -- the standard iPod video settings worked like a charm (we had 900kbps and 30fps encoded by Xvid).
Some have even gone as far as to state that Sony's strategy of using MPEG-2 and uncompressed PCM audio on single-layer Blu-ray discs may have required too much video compression, resulting in early releases that don't match the sharpness of VC-1 encoded movies available on HD DVD.