There are several options. With DNN 6.x or higher, you should usually use the client resource management API to register files. It is really very simple since you just need to register the control:
<%@ Register TagPrefix="dnn" Namespace="DotNetNuke.Web.Client.ClientResourceManagement" Assembly="DotNetNuke.Web.Client" %>
And then include the specific file:
<dnn:DnnJsInclude runat="server" FilePath="jquery.cycle.min.js" PathNameAlias="SkinPath" />
Usually we do this through the skin, because we make custom skins for most of our sites, or if we create a custom module that needs a plugin, we will do this in the corresponding ascx file for the module.
If you need only a plugin on a specific page, and not for a specific module, the best place to add it can be found in the section "Page Settings → Advanced → Page Title".
You can find out more here: http://www.dotnetnuke.com/Resources/Wiki/Page/Client-Resource-Management-API.aspx
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