JScript.NET was dropped for .NET 4.0; it has always been a bit of a curiosity though. I think it was there because "classic" ASP had support for doing server-side scripting in JScript, so somebody thought ASP.NET needed to support it also. Thankfully, there are a few alternative JavaScript implementations on .NET such as IronJS.
http://msdn.microsoft.com/en-us/library/ms974588.aspx
I haven't seen it used anywhere as a server side application, though.