well, now that i think about it some more,
Open Source Server Software or not, chances are, your application is still open source. (Perl, ASP, PHP, JSP, whatever) though this is the part that usually no one knows about since its all custom to your site, there are lots of pre made scripts out there for every platform that poeple install on thier site.
Problems with this is other poeple see you are runing that app, go and download it too, and look at it locally, now they know exactly what code you are running, and they know the directory structure, for example, If I went and bought fusetalk, I would easily find out where tha admin directory is on forums.anandtech.com, of course i dont know the password, but if i were the admin, id rather poeple not even know where to try. And seeing exaclty how these scripts are run would give someone insight to a lot of possible holes, APPLICATION holes, not server holes, which IMO, are much more of a threat, and im betting there are many more of these out there.