Well, PNG is for stills -- for stills, PSD will also preserve alpha (it's what I use and then I construct sequences inside of Premiere or After Effects).
Not sure if there is any video codec that preserves alpha right now in AS.
I'm using a two pass render. One on a image for eye blinks, mouth movement and expressions. The second for head tums. The underlining bones don't effect the bones on the second pass.
Just slightly off topic, but is there an avi codec that supports alpha? The video editor I usually use can't import quicktime (well, it might be able to using AviSynth, but I don't know how).