ProgramGood.Net

http://www.sitefinity.com/devnet/forums/sitefinity-3-x/developing-with-sitefinity/javascript-files.aspx

<script src="<%=HttpContext.Current.Request.ApplicationPath.EndsWith("/") ? HttpContext.Current.Request.ApplicationPath : HttpContext.Current.Request.ApplicationPath + "/" %>Res/Scripts/jquery-1.3.2.min.download.js" type="text/javascript"> </script> 

I had a strange bug in Chrome where the css didn’t load properly using this in the masterpage.

<Scripts>
           <asp:ScriptReference Path="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js" />
           <asp:ScriptReference Path="~/javascript/jquery.colorbox.js" />
</Scripts>

This may have been a timing issue as I am now getting jquery from my website and not google.