Today I upgraded wordpress again,
All I did was upgrade wordpress via emerge (this happens automaticly when running emerge -uND world 
), run webapp-config -U -h blog.leipie.com -u apache -g apache -s apache wordpress 2.8.1, run CONFIG_PROTECT="/var/www/blog.leipie.com/htdocs//" etc-update and execute http://blog.leipie.com/wp-admin/upgrade.php in my browser. Et voila, it was done.
I first made a backup off my mysql data just to be sure. using tar to backup my wordpress db in /var/lib/mysql
Edit: Did the same for 2.8.3 today, but this has overwritten wp-config.php 
Luckily I keep a backup…