The Debian package, which is also found in Ubuntu, does some odd things to MediaWiki to fit in with the odd things Debian does to Apache.
This page should list those changes, for the benefit of end users coming from using a tarball.
- pkg-mediawiki-devel list at Debian
The 1.19 package in Wheezy and Quantal is quite close to the upstream tarball and you can use it in confidence. Previous distro versions of MediaWiki in Debian and Ubuntu are not recommended, and you should use the tarball instead.
Specified versions will be maintained as long-term supported (LTS), with support from WMF and the distro packagers. The first release so blessed is 1.19, which is in Debian wheezy and Ubuntu 12.10 Quantal.
Debian changes to Apache 
README.debian details much of what you need to know.
- httpd conf in /etc/apache2
- htdocs in /var/www (default)
- logs in /var/log/apache2 (default)
Sysadmins coming from using Apache tarballs should read this page.
Debian changes to MediaWiki 
- The package chooses PostgreSQL over MySQL due to a packager's personal preference (despite being aware that MediaWiki is written to MySQL and Postgres is an afterthought).
- The package is maintained primarily with a view to being a component of FusionForge, rather than as a standalone for people who just want to install a wiki.
- Apache rules are added in /etc/mediawiki/apache.conf
- The installer tells you to move the wiki configuration to /etc/mediawiki/LocalSettings.php
- The MediaWiki code is in /usr/share/mediawiki/, but
- LocalSettings.php and AdminSettings.php are symlinks to /etc/mediawiki/LocalSettings.php and /etc/mediawiki/AdminSettings.php
- config/, extensions/, and images/ are symlinks to /var/lib/mediawiki/config/, etc.
- /var/lib/mediawiki/ has config/, extensions/, and images/, along with symlinks back to /usr/share/mediawiki/includes/, /usr/share/mediawiki/index.php, etc.
- The Math extension is no longer shipped as core in upstream tarballs, and consequently not in the Debian package. It is in the mediawiki-extensions-math, and enabled with mwenext math.
- todo: mediawiki-extensions
If you install MediaWiki from tarball anyway 
If you really want to use the MediaWiki tarball (e.g., you want the very latest MediaWiki, or you want to test a beta), installing the MediaWiki distro package can be very handy for pulling in prerequisites.
See also 
- Manual:Running MediaWiki on Debian GNU/Linux - hopelessly outdated (talks about 1.7)
- Manual:Running MediaWiki on Ubuntu - hopelessly outdated (talks about Ubuntu 8.04)
- Manual:Installing MediaWiki on Ubuntu 10.04 - hopelessly outdated and marked accordingly, recommends against distro versions
- Manual:Installing MediaWiki on Ubuntu via GUI and Synaptic - outdated, recommends against distro versions
- Manual:Installing MediaWiki on Ubuntu 11.10 - says "the 10.04 page worked fine for me".