On a recent project I have been working on in C#/ASP.NET I have some fairly complicated JavaScript files and some nifty Style Sheets. As these script resources grow in size it
Not a perfect answer, but if you're using MVC4 they've built this in as a new feature. When running a Debug configuration, it outputs individual files with comments and such but when you switch to Release, it will automatically bundle, minify, and change in page references to the minified files. You can setup separate bundles for, say, jquery and your own js. This works with CSS and JS files.
http://www.asp.net/mvc/tutorials/mvc-4/bundling-and-minification
If MVC4 doesn't work for you, you can also find packages on Nuget that can help such as this:
https://www.nuget.org/packages?q=minify