To register a js programmatically, use the following:Page.ClientScript.RegisterClientScriptInclude("script1", ResolveUrl("~/include/js/javascriptfile.js"));.
This can live behinde the master page inside the load event.
//Its better to check if the script was registered (Page.ClientScript.IsClientScriptBlockRegistered("script1")).
Also, you can use another way if you have more script to register which in sequence:
if(!IsPostBack && !Page.ClientScript.IsClientScriptBlockRegistered("URLs"))
{
StringBuilder scriptBuilder = new StringBuilder();
scriptBuilder.Append("<script type='text/javascript' src='");
scriptBuilder.Append(ResolveUrl("~/include/js/mmloadmenus2.js"));
scriptBuilder.Append("'></script>");
scriptBuilder.Append("<script type='text/javascript' src='");
scriptBuilder.Append(ResolveUrl("~/include/js/mm_menu.js"));
scriptBuilder.Append("'></script>");
scriptBuilder.Append("<script language='JavaScript1.2'>mmLoadMenus();</script>");
Page.ClientScript.RegisterClientScriptBlock(typeof(System.String),"URLs",
scriptBuilder.ToString());
}