for as long as i remember (certainly through several different browser-changes) pure-data's website has popped up an annoying dialog on first visit:
i know it happens with at least firefox and opera. upon choosing to install the certificate despite the browser's initial objections, you can continue.
not dealing with SSL regularly, perhaps a different one could be generated for each domain, and some kind of switch statement in the apache/lighttpd/whatever conf could send the right one...