mupen64plus was accepted by ftp-masters and will hit the archives soon. The debian package needed some adjustments to be accepted. This means that glN64 had to be removed because it is not distributed under a dfsg compliant license. If anyone knows Orkin then please ask him to contact the mupen64plus team.
All other changes shouldn't be that visible for users. Some bugs were fixed and some libraries were stripped from the build process and replaced by official packaged ones. It builds on many different architectures, but as x86 and amd64 are the only supported architectures by upstream the experience will differ.
Upcoming stuff for debian are:
a port to xz-utils for lzma support. This currently depends on liblzma in unstable, but the patch exists and was already send to upstream and will automatically add support for lzma2 and xz.
Making it compliant to the XDG Base Directory Specification would be nice for save states, rom cache and configuration files. There is already a libxdg-basedir package in debian, but I haven't read the documentation yet.
Last but not least: fixing more bugs.
Upstream is also starting a big rewrite to seperate gui from the rest (so no more gtk/qt specific stuff inside plugins), make most of the code platform independent and splitting everything to be more modular. Also some low level plugins are currently developed inside their trunk. So it looks quite promising for the future. But please don't ask to package the qt gui before the rewrite has been merged.
Before I forget it: Congratulations to Tobias for your first package in Debian (and in Ubuntu Universe after their sync with debian).