A recent move of my server from a public server to a self hosted server in Ubuntu had turned into a problem solving challenge. I had build a new Ubuntu server with webmin as a hosting manager. A current live version of Joomla was moved over to this server, and all of a sudden the SEF stopped working. I am currently a user of SH404 with JoomFish, and everything worked before. Now I got 500 error even in the admin screen. I made sure the naming convention is right, .htaccess was typed correctly. The main error was that by default apache does not turn on mod_rewrite, to do that in a Ubuntu or Redhat server all you have to do is type
sudo a2enmod rewrite
and restart the apache server by typing
sudo /etc/init.d/apache2 restart
This should fix all those errors when migration a CMS to a new Ubuntu server.
Enjoy