For Windows, I hear good things about Jahshaka, but haven't really looked at it yet, same with zs4 http://www.zs4.net/
I took Wax for a spin a while ago and it was impressive for the price (free) http://www.debugmode.com/wax/
Otherwise I'm not really up with the free software available on the PC, I'm sure there must other open source or cheap compositing packages for windows?
Otherwise you could do them a frame at a time, using virtualdub to export them and a free paint package like gimp to paint each frame.