Right now, subdomains are done by making a DNS entry, waiting for that to resolve, then using Mod Rewrite to do the URL rewriting.
while this works as its sopposed too, its slow and using mod rewrite causes complications if i want to use rewrite rules on a sub-domain (an example is using wiki on a sub, wiki.example.com, with rewrite rules to change index.php?title=Foo to wiki.example.com/Foo).
I understand that part of this is to make things simpler in the administration side, but a long time ago in a galaxy far far away (well, when i was at school). i wrote a simple control panel for another server that stored all domain/client info in a db and then various tools read from the db (and i used bind 
)
I had a similar setup with the conf / conf.d directories but i also had
the conf.d had a couple files
conf.d/vhosts.conf
conf.d/global.conf
the global.conf had global options (such as aliases for webmail, qmailadmin, etc)
the vhosts.conf file had nothing more than
this domain
namevirtualhost Ip
include conf.d/domainname/*
and so on for each domain
conf.d/domain/ that had files like
domain.conf
subdomains.conf
options.conf
sub domains used vhost containers and i could chose any directories for my subdomain (not ~/example.com/html/sub for sub.example.com)
I had a simple php script that created/edited/deleted files as need be.
also, djbdns supports wildcard entries but the interworx panel does not let us use *
using * IN CNAME domain.com. and <virtualhost sub.domain.com> would allow us to use rewrite rules in subdomains AND provide us with instant sub-domains instead of waiting for dns to be reloaded from cron and then the record propogated around.