I took one of your videos and did a rough roto job just for illustration purposes, encoded to vp6a, then wrapped into .swf with adobe flash
You have access to vp6a with Adobe Media Encoder or After Effects. If you're keying in AE, I'd recommend exporting a lossless format with alpha (e.g. uncompressed,
huffyuv, ut video codec), then use AME (because AE only does 1 pass encodes, but you can do 2pass and have more options with AME)
I included a html file so you can play with it offline locally and see what's going on
note - some flash front ends do not support alpha channel (e.g. some versions of JW didn't for a while), or they need special code to allow for transparency
(see attached zip file)
There are many tutorials out there, for example here is a older pdf you can download with illustrations:
http://www.scienceandart.org/Transpa...l%20by%20R.pdf
Cheers