Although I do not like ad popups myself, this plugin was so similar to my "delete control" plugin that it was simple to implement. If you want to do this, here's a plugin to do it.
The proposal thread is here: http://forum.coppermine-gallery.net/index.php?topic=29218.0
Basically you set 6 links in codebase.php and a "popup every X clicks" in the configuration option in codebase.php. Then every X clicks on displayimage.php, a popup window appears, with the link being one of the 6 you set. The 6 links are cycled through.
There's a README with information. Admins in "admin mode" will not see the popups. Change to "user mode" if you want to test things out. In general, you should also log in as a non-admin user to check things out.