It comes down as mentioned earlier whatever you're most comfortable with. My work focus on Windows Server, most of them have no idea about Unix / Linux and I have to admit I am not the best Linux Sysadmin but I can work my way around it so they tend to ask myself for some help on adhoc request. It also depends on the environment, most of our stuff runs on Windows and all the backup software runs on Windows, we can also do certain things quicker using Windows and the fact it runs on an AD environment certifies a need for a majority of Windows for LDAP capabilities.
I like both, Windows is a bit easier to use in terms of the GUI but I am not overly keen on Windows 2012 over Windows 2008. But I like both, for me it really just depends on the use. I tend to focus Linux servers on web servers and mail/proxies whereas Windows for things like SQL which a GUI is much more helpful for.