I haven't found that many differences from running IIS or QVWS as webservers for QlikView.
Some clients might prefer IIS, as it is familiar to them, might simplify support and maintanance.
IIS allows for greater security and settings control, while QVWS settings are pretty basic. You can also host custom ASP/.NET applications with IIS.
As for configurations, you can check the Server Reference Manual for more information.
I agree with Daniel.
What I have found however, is that QVWS uses far more memory than IIS when many users are connected.
This is a bit tricky to measure, but we used HP Load Runner for simulating user logons and simulated 3000+ logged on users on a 300Mb QV doc.
I'd add the obvious part that is that if you already have a IIS running, and all your Active Directory users have their permissions configured here, you should think of using IIS instead of the QVWS.
On the other hand, there are some features supported in IIS that might help you deploying to different devices, for example, the client certificates mapping authentication for users integrated in Windows.
Configuration as far as QlikView is concerned is quite trivial, as Daniel says, they are well described in the Server Reference Manual, although the network and systems configuration may require additional stuff to get QlikView Server listening and working (.NET 4, firewalls, proxies, etc).
What you should really ask is what are the characteristics of the deployment, complexity of the network, number of concurrent users, size of documents, scheduled tasks... and choose accordingly. The more complex it is, the better IIS might perform, and viceversa. In short, I dare say QlikView WebServer is just a small webserver, whilst IIS is a very complex, highly customizable web server, that is in addition integrable with the AD.
Hope that makes sense.