The one in the System.Web.* namespace is a clone of the one in the Microsoft.Security.* namespace, but the System.Web one is slightly tweaked for better performance characteristics. We recommend the System.Web one going forward.
If you set the <httpRuntime encoderType>
setting as described at http://www.asp.net/aspnet/overview/aspnet-45/whats-new#_Toc318097382, then you can just use the built-in encoding routines like HttpUtility.HtmlEncode, and the implementation will be provided by the Anti-XSS libraries.