Thanks for your response 
I've been pushing to take back the root domain, but have so far hit resistance. Perhaps I can convince people to at least give it a try.
As far as moving everything into sub-folders of the root domain, as opposed to an obscene amount of sub domains, we could give that a try for some of the sub domains, but not all of them. Unfortunately, several of the sub domains are _extremely _large sites that require a lot of processing power on the server. Nearly every single one of these sites has it's own dedicated server. I think it would be heinous to move them all - but I will see what we can do about moving some.
Thanks again! 
