Well, this is not a ispconfig related bug BUT we are using fastcgi as default php mode for apache.
The fastcgi FcgidIdleTimeout Directive takes no effect (deafult is set to 300 seg). This issue causes that php-cgi process are always on memory ignoring the idle timeout. High numbers of process = lack of memory = ...
If we set a value manually in the apache directive or in the .php-fcgi-starter file for the site it work and process are close after the idleTimeout.
I found this issue in Ubuntu Server 10.04.3 LTS, libapache2-mod-fcgid 2.3.4-2
Please check it