I had a problem where I wanted to use the intellisense version of JQuery when I am writing the code, the normal version when I debug it and the minified when it actually hits production.
I also wanted all this done on my master page so the path to the js file had to be relative to the site root and not the page it was defined on.

I found the solution here:

http://damianedwards.wordpress.com/2009/03/28/setting-up-jquery-for-aspnet-web-forms-projects/

It essentially revolves around using the script manager to reference the JS files and using naming conventions so it knows which one to open where.

Edit: Don’t forget to download the hotfix or the -vsdoc won’t work.

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