<p>I have extensively used Prototype before and it helped us add considerable interactivity to our web applications. However we are looking at making the move to use jQuery in order to standardize on something better supported in Visual Studio.</p>

<p>I understand that we can use the jQuery.noConflict to run it alongside Prototype, but we would like to avoid having users need to download both libraries to use our website.</p>

<p>So, is there a good resource that can help us move old scripts from Prototype to jQuery?</p>

I can't really help you too much with your question, other than to say that I haven't heard of any such tool, and that I'd be really surprised if one actually existed.
While I think jQuery is a great library, and that you're right to be wanting to only use one library, just remember that the cost of you changing over all your scripts is going to be many many hours of work. The cost of your users downloading an extra 30kb of scripts is going to be roughly 0.3 seconds. Perhaps try to slowly phase out Prototype and only refactor your existing pages when a) you have to, or b) if you've got nothing better to do.