Yes, .png contains an alpha channel and is fine for the individual frame files. Sadly, rendering to Quicktime doesn't retain the alpha channel, and the default Grey seems to comprises of 2 shades of grey so using it as a mask gives screened results. I haven't tried another "Green Screen" type colour yet, but there's no reason it shouldn't work. I use the Open Image Sequence of Quicktime Pro all the time, it's great for comparing subtle lighting changes across a range of renders. In P6, I find the slider in the render panel frightfully slow.