Here is the code I use within the codebehind. (C#)
modPath = this.ModulePath;
if (!Page.ClientScript.IsClientScriptIncludeRegistered("calendarDateInput"))
Page.ClientScript.RegisterClientScriptInclude("calendarDateInput", modPath + "calendarDateInput.js");
Note that this loads a JS that is in the same directory as the module (modPath) and puts it in the same place that DNN does (Not in the head, but at the top of the form). In addition, if you have more than one instance of said module on a page, this will ensure that the Javascript get's loaded only once.