mojoPortal is built on ASP.NET so you use the same techniques to add javascript in mojoPortal that you do in ASP.NET
Example:
this.Page.ClientScript.RegisterClientScriptBlock(
typeof(ExtBasePanel),
"ext-all", "\n<script type=\"text/javascript\" src=\""
+ ResolveUrl(extJsBasePath + "ext-all.js") + "\" ></script>");
there are also other script registration functions built into the page like .RegisterStartup(...
Hope it helps,
Joe