I\'m fairly new to ASP.NET MVC, and I\'m having a little trouble with scripts... in particular, I want to use jQuery in most pages, so it makes sense to put it in the master
You should take a look at using a utility like squish it. It can aggregate and obfuscate all of your css and js files for you. Or you can use it to generate script tags if you just keep it in debug more by using ForceDebug()
http://www.codethinked.com/squishit-the-friendly-aspnet-javascript-and-css-squisher