I'm having trouble with open_basedir. I just discovered the following while randomly checking my PHP error log:
[25-Apr-2012 10:49:58 UTC] PHP Warning: is_file(): open_basedir restriction in effect. File(/var/www/user_name/example.com/track.example.com/piwik/plugins/GeoIP/libs/GeoIP.dat) is not within the allowed path(s): (/var/www/user_name:/usr/share/php5:/usr/share/php:/var/run/mysqld) in /var/www/user_name/example.com/track.example.com/piwik/plugins/GeoIP/GeoIP.php on line 317
The real name does contain an underscore. So, as is clearly visible, the file is inside one of the allowed directories.
The php.ini looks like this:
open_basedir = "/var/www/user_name:/usr/share/php5:/usr/share/php:/var/run/mysqld"
PHP is invoked by Apache 2 via fastcgi.
Update: Oh yeah, almost forgot: The /var/www directory is a bind mount.