How bout a program that would build a .upgrade file from the official SB .upgrade. It could also allow you to select what apps to install on your empeg.

This sounds like a great idea. Unfortunately, the vast majority of the software distributed in the .upgrade file is in the form of an ext2 filesystem image. In order to make a new .upgrade file that contained additional or different software, you'd have to be able to create populated ext2 filesystem images. While this is trivial on most Linux machines (through the use of the loop device), it would be nigh impossible on Windows machines, which would be the most significant part of the target audience for such a monster.