Aegir Virtualhost files on Ubuntu
Just a very quick note, as I had to do a bit of hunting to find where the heck Aegir was generating my virtualhosts for all of the domains I was managing through it.
By default it is located in
/var/aegir/config/server_master/apache/vhost.d/, where that server_master part might change depending on what host you're modifying (if you're in a complex hosting situation, for example).
This comes in handy if you want to install SSL certificates yourself instead of going through Aegir to handle the certificates.