It was challenging to find an elegant solution to this simple problem. If you need to select a particular ASP.NET checkboxlist listitem in jquery by passing in the value you want to select, use the following.
ADD CLIENT-SIDE READABLE VALUES TO THE CB INPUT WRAPPER SPANS ON THE SERVER SIDE: 

 For Each li As ListItem In CheckboxList1.Items
        li.Attributes.Add("itemValue", li.Value)
 Next

AND ON THE CLIENT ADD A FUNCTION TO FIND THE VALUE IN THE SPAN, 
THEN CHECK DESCENDENT INPUTS:

  function checkListItem(targetValue){
      $("span[itemValue*='" + $.trim(targetValue) + "'] input").attr('checked', true);
    }