Debian
The Debian project uses the criteria laid out in its Debian Free Software Guidelines (DFSG). The only notable cases where Debian and Free Software Foundation disagree are over the Artistic License and the GNU Free Documentation License (GFDL). Debian accepts the original Artistic License as being a free software licence, but FSF disagrees. This has very little impact however since the Artistic License is almost always used in a dual-license setup, along with the GNU General Public License.
Regarding the GNU Free Documentation License, Debian decided to apply the DFSG to everything in their distribution, including documentation. The FSF argues that documentation is qualitatively different from software and is subject to different requirements. The end result of a long discussion and the eventual vote in Debian was that the works licensed under the GFDL are considered free as long as they do not contain unmodifiable sections (what the GFDL calls "Invariant Sections"). Most GNU documentation includes Invariant Sections.
Read more about this topic: Free Software Licensing