There is "Lodestar Live" free software that originally came out for Lodestar camera's only, but now supports many more cameras. It does stacking on the fly and can subtract darks as well.
Stargazers Lounge has a large number of followers of this software if you want more up to date information.
EDIT: For anyone interested in this software, it has now been taken over by Starlight Express and the software is now called Starlight Live.
http://www.sxccd.com/drivers-downloads