Bear in mind to transfer files between any Windows machines you have on your network and your Linux box you would probably be best setting up a Samba server on the Linux box to provide a centralised file repository. It's very well documented and isn't too difficult to implement.
Ease of use
In a server environment you would want to install Linux without a GUI, this means no point and click configuration. Frankly speaking, if you're setting up a server you wouldn't want this, a GUI adds unnecessary overheads and usually your servers are remotely accessed using a text only terminal anyway via SSH. You wouldn't want your only choice for remote administration to be a remote session over something like RDP or VNC.
Of course this adds a level of complexity, you have to learn to use the command line. On the other hand package managers take a lot of the effort out of installing software. Instead of searching around for that .exe file to install Apache for example you would simply type:
[code:1]apt-get install apache[/code:1]
Not to mention driver support, a LOT of drivers are already integrated, most of the time you will never have to search around for drivers.
Quality
Overall you're going to get stability that surpasses any Windows based operating system, it's not unusual for servers to have an uptime of several years. I just logged into one of my companies hosting servers and it currently has an uptime of 502 days, this is actually pretty typical.
A lot of the software available for Linux has been in development for many years, some of it is older than I am! Overall you get the benefit of open source software, many people can observe code changes, identify bugs within software and contribute fixes.
Security
This is where Linux really surpasses Windows, most of the viruses out there have absolutely no effect on Linux. The inbuilt firewall (IPTables) is incredibly powerful and the protocols used for administration are very secure.
Compatibility
Windows applications can be run on Linux using a program called WINE, in a server environment it's unlikely you will ever need to do this. In most cases there are alternative packages that will do the same thing natively on Linux (and in many cases do it better).
Debian has over 30,000 packages in it's repositories, it's fairly unlikely you won't find a package that will do what you want. I use Debian as my main operating system and I do all my development work on it, it gives me far more flexibility than any Windows based operating system.
Distributions
Linux comes in many different types, choosing a one can be difficult, I've listed a few below that you may want to check out. For an overview of a few operating systems check out
http://www.distrowatch.com.
Debian -
http://www.debian.org (My personal favourite and my main operating system)
CentOS -
http://www.centos.org (A lot of people use this, I personally don't like YUM package management)
Ubuntu -
http://www.ubuntu.com (A good starting place for beginners, though not really a server OS in my opinion)
If you're wanting to get to grips with it I highly recommend grabbing yourself a copy of Ubuntu and installing it on a second partition and start messing around, there are loads of resources about setting up a LAMP (that's: Linux, Apache, MYSQL, PHP) environment.
Of course if your website is ASP based you will be forced to go for a Windows based server.
