I’ve been toying with the idea of a general binary patching system for a while and have finally decided to do something about it. I’ve registered a project @ SourceForge called ediff (check it out at http://sourceforge.net/projects/ediff ) which could provide support for .deb files (being a Debian user myself, I _definitely_ want to be able to support .deb files eventually)
The basic idea of my project is to extend diff & patch to support any file type by means of modules which know how to analyse specific types — e.g. for text files, you could use the current diff & patch, there’d be a module for zip files, tar files, deb files…. whatever anyone wants to write a module for. If anyone’s interested, take a look: will hopefully start actual development in a few weeks.