I would like to use some kind of virus protection on the server. What options do I have? I installed MS security essentials, but I just learned that I is not for commercial/government use.
If you're a fan of MSE, I would suggest Microsoft Forefront.
The commercial version of Forefront is now available: http://www.microsoft.com/forefront/endpoint-protection/en/us/default.aspx
There are a lot of other products as well that Google will help you find.
There are numerous options available for those who do not meet the licensing requirements of Microsoft Security Essentials. One is the Microsoft Forefront products while other products which could be used sold by companies such as Symantec, CA, etc.