Question

So I only want this JavaScript to be included in the response to the browser
if ViewBag.L1Cat does not equal null. At the moment I am getting the error:
cannot perform run time binding on a null reference. And the debugger
does not want to stop inside the if statement for some reason. ViewBag was
populated with respective keys\value pairs in the action method that returns
the view.

 <script type="text/javascript">
 @{
    if(ViewBag.L1Cat != null)
    {
       <text>              
          var FirstLevel = 
                    $('#MenuContainer')
                       .find('.FirstLevel')
                       .attr('@(ViewBag.RootCat.ToString());');
       </text>        
     }
   }    
 </script>

Answer 1

Is it absolutely necessary to omit the code?

You might find it cleaner to take this approach:

<script type="text/javascript">
var doStuff = @(ViewBag.L1Cat != null ? "true" : "false");
if (doStuff)
{
var FirstLevel = $('#MenuContainer').find('.FirstLevel').attr('@(ViewBag.RootCat.ToString())');
}
</script>

Alternatively

<script type="text/javascript">
@if(ViewBag.L1Cat != null)
{
 <text>              
  var FirstLevel = $('#MenuContainer').find('.FirstLevel').attr('@(ViewBag.RootCat.ToString())');
 </text>        
}
</script>