If your users are unable to connect to DirectAdmin on port 2222 due to firewalls or proxies. It is still possible to setup apache to allow DirectAdmin to run through apache using its proxy options.
As soon as you enable Pigeonhole with Exim and Dovecot you get email quotas not working any longer. And here is a way how to enable them back with Dovecot.
If you sell additional IPs to your users, so they could connect remote servers from your hosting server using their dedicated IP as a source IP, you might want (or even need) to protect it from hijacking by other customer of yours. So nobody else could use it.
It was mentioned somewhere that to have session.save_path pointed into /tmp is not very secure, as a hacker with a hosting account on your server might hijack a session file from a neighbor site, if he (or she) manages to get list of files located in /tmp. To prevent this you might want to store sessions under user's home directory.
If you decided to use Modsecurity on your server with DirectAdmin, there is sometimes a need to disable the module for a particular domain (virtual host). And here I'm going to describe how to achieve the desired.