Hi,
There is no way of using server side includes with Dynamics CRM2011 since you may not use custom ASP.NET code (the ISV folder is deprecated and also would not work with CRM Online).
You could include a reference to Requiresjs and use that to load all your dependant scripts. (http://requirejs.org/) or HeadJs (http://headjs.com/)
Make sure that you understand the client side caching of web resources - www.develop1.net/.../CRM-Developer-e28098Must-Knowe28099-2-Web-Resource-Caching.aspx
hth,
Scott