Personally I would not use IIS for any tasks even if the company had paid for it... To an extent I don't care which is faster, it is only a few extra connections one way or another anyway... my problem with IIS is firstly its track record is very poor and secondly it is overly-complicated. With Apache (one windows and Linux) you have folders for this and that and you can see plugins and remove them. That means you have complete and total control of what plugins are running on your server and can view it just as easily... with IIS you have an insane hieratical system where you have no clue what components are interfacing with your server.

Here is a basic off the top of my head list:
- Security (Apache is more secure)
- Control (Apache gives greater control, nothing to do with OSS)
- Automation (Apache has plain-text configs, automation is easy)
- Separation of system security / web-server security (If you add a new user to a Windows/*Nix system that does not effect the web-server)
- More Modular (You can add and remove stuff more easily)

I am not even going to pick at the free FTP server, it is too easy! That thing should just be removed.

Microsoft's engineers don't think stuff though enough and just keep building more components on old ones and cross linking until we reach a point where, if one component high up the chain has a problem the entire tree inherits it.

Also, linking a web-server / FTP server into a domain is NOT a good idea and NEVER was.