Autopano Giga does all the blending itself but it costs $ try Microsoft ICE Image Composite Editor it is free and does a pretty good job until you get to 1000 images or so. The right click on your images and Stitch using ICE is a nice touch as well if you use PC.
ICE might be the best ever Microsoft product and they give it away free
http://research.microsoft.com/en-us/.../projects/ice/