One useful tool we recently started using is etckeeper.

It provides version control over your /etc/ directory, which may prove quite useful when you maintain system in co-op way with your customers. Etckeeper also comes with hooks for apt, so even if you use it terribly it does give you an insightful history of when which package was installed.

Installation and setup in Ubuntu:

apt-get install git etckeeper
# change VCS in /etc/etckeeper/etckeeper.conf to git
etckeeper init
etckeeper commit

And your ready to go. Proves to be great for "MySQL tuning", webserver config changes and firewall edits. Little effort and nice to have as an addition.