You can simply run the javascript you need from the display HTML of your user control.
<a href="javascript:doSomething();">Click Me</a>
From the sounds of things you want to create some form of controller in JavaScript. When the page loads each of your control registers by the controller. Then the action in one of your controls performs a function on the controller, which does something with the controls registered with it.
Your JavaScript may be as simple as:
var oControls = new Array();
doSomething = function () {for (var i = 0; i <oControls.length; i ++) {var oControl = document.getElementById (oControls [i]); oControl ......}}
So, you need to register your control using the ScriptManager in the method of rendering your users.
ScriptManager.RegisterStartupScript(Me, Me.GetType(), "Startup", String.Format("oControls.push('{0}');", ClientID), True);
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