For quite a while now there has been work towards bettering the Debian source package format, in particular with more effective handling of Debian packaging files, and this resulted in a new source format coming about: 3.0 Quilt.
This new system integrates a patch system into dpkg-source, which ended up being based upon Quilt. Besides the 3.0 Quilt format there is also a 3.0 Native format being worked on that is more similar to the original 1.0 source package format.
The 3.0 Quilt format adds support for BZIP2, LZMA, and XZ compression, which is superior to only Gzip found with the 1.0 specification. The 3.0 Quilt version also supports multiple upstream tarballs, can include binary files with the Debian packaging, can automatically replace the Debian directory in the upstream tarball, and is capable of creating a new Quilt-managed patch in the Debian patches directory when changes to upstream files are detected.
The 3.0 Native format only brings the new compression formats (BZIP2, LZMA, and XZ) on top of the 1.0 source format and excludes by default files that should not be part of the tarball.
Work on this new Debian source format is not expected to be complete until June of 2013, but you can read about all of these details that were just blogged about by Raphaël Hertzog
. There are also other details to be found on the Debian Wiki