I have a use case where we will have an ASP.NET MVC Server Application but it needs to talk over a persistent connection to a Windows service. It doesn't look like SignalR does this as it really wants talk Server to JavaScript browsers but I did notice .NET desktop libraries. Can it talk from a server to a Windows server? If not, is there a recommended way, TCP/IP or HTTP to have a persistent connection between the two? NetTcpBinding in WCF?
Yes, there is a SignalR client library for .NET that you can use in any old .NET app to talk to a SignalR server just like you can from JavaScript.
While there is a WebSockets binding for WCF, there is no binding that actually talks native SignalR which adds its own message framing on top of raw web sockets. So, while possible, it doesn't exist today and I wouldn't hold my breath for it ever being created.