A crashed server at a friend's reminded me of the importance of backups. Regular backups are in place of course, but scattered throughout /var/www, /media, /var/lib/mysql, etc. The FHS recommend to put everything in /srv/[protocol]. This should make backups a lot simpler because only /etc, /home and /srv need to be saved.
I changed the paths earlier today. Everything should still work fine and soft links for backwards-compatibility are in place for now. Please report any unexpected problems.