Here is our department breakdown,
IT Help: This is where staff/faculty from our college call for computer issues, new programs and stuff like email setup. We have 2 staff and 1 or 2 students in this group.
Web Dev Team: I am part of this team of 2, soon to be 3, people. We handle all of the websites and choose what CMS to use for certain projects. We also handle any external web apps to integrate or create.
Communication Team: One aspect of this group plays a key role for our website. Our comm team is in charge of what is presented to the public whether it be from a website/twitter/facebook. Our graphic designers work on this team as well so any designs/logos come from this team.
What an excellent question. I'm surprised there aren't more responses!
I think we at Eastern Mennonite University have successfully implemented Zeldman's suggestion. We have had a Web Work Team in place for nearly 10 years. It's now comprised of a team of awesome web programmers (currently there are four) and the director of IS, as well as the director of marketing and her web content manager/strategist (me) and designer/social media coordinator. We meet monthly and also process issues via email and IM frequently.
The campus community goes to the IS helpdesk with issues like computer problems, new programs, email admin. We in marketing have a similar hotline to the web programming team (Application Development, they are called, or AppDev) except the programmers are not viewed as a vendor. Rather, our hotline activates a ticket within their project system and they can then track it and resolve it in a priority fashion. It's another way we communicate in between meetings, since our offices are across campus. We also talk frequently via IM. It's mostly used for smaller site issues.
The marketing department maintains the public website and cotent, while the AppDev team maintains the portal site. We interact frequently with each other on both, though, and do not have an issue with territorial behavior. Maybe we're too busy. :-) We have an amazing set of people working here, with many different skill sets and responsibilities, and really have come to rely on our Web Work Team structure since it brings us together and seems to work well now.
We started in IT and moved to Communications/Marketing. Because of the way this particular university runs, it was a good move for us (IT is understaffed and underfunded). I still yearn for the Greenfield/Zeldman concept of an independent division - but realistically I don't see it happening here any time soon.
I know there's been at least one large survey on this topic but now I can't find it. :/