My thinking is that I'd like to just load all of the .js files in _Layout.cshtml, and that way I know it's loaded once and only once. Also, the client should only have to download this file once as well. It should be cached and therefore shouldn't really be a performance hit, except for the first page load.
I should probably note that I am using ASP.Net bundling as well and loading most of the jQuery/bootstrap/etc from CDN's.
Is there anything else that I'm not thinking of that would cause problems here? Should I bundle everything into a single file?