After upgrading to 4.3.0 I am now getting this error from effects.js in the Script.aculo.us library

Error: $(element) has no properties
Source File: effects.js
Line: 76

Which would be:

Element.getInlineOpacity = function(element){ 
  return $(element).style.opacity || '';
}

Any thoughts on what might have changed, and what I can do to correct it. Thanks in advance.

What is the suggest course of action if we are using other .js libraries that also emplore the $(element) functionality? The two are not playing nice at all.

Well Script.aculo.us uses the prototype library as well, so I am not sure it why it is not handled since you say you specifically tested against Atlas & Prototype. I think it is a little unreasonable to perceive that no one will ever use another library that has $(element) since as you noted the big boys already have this built in. I did already read your blog post, and probably should have thought of this before this point, but it never occured to me (I am no js wizard such as yourself;). As to how to resolve this issue I am unsure, would it be possible to add some check to your routine

//-- prototype/atlas shorthand functions
function $()
{
  var ary = new Array();
  for (var i=0; i<arguments.length; i++)
  {
    var arg = arguments[i];
    var ctl;
    if (typeof arg == 'string')
      ctl = dnn.dom.getById(arg);

    if (arguments.length == 1)
      return ctl;

    ary[ary.length] = ctl;
  }
  return ary;
}

to check and see if other libraries are loaded before calling this functionality. I have been looking at this, this morning and it seems the problem is that the dnn client api picks up the $(element) first, and has already performed its duties by the time it passes control off to Script.aculo.us. I can provide you with a module using Script.aculo.us to test this if that is helpful.