I am not good at jQuery so I am not sure if my assumptions are corrent.
I am using the isotope plugin, with which I want to insert elements one by one (and not every
$("#items_are_here").find('.item').each(function( index ) {
     setTimeout(function() {
            $('#container').isotope( 'insert', $(this));
         },3000);
    });
in the above context, $(this) is the window object, because it's inside setTimeout.
Modify your code to and try:
$("#items_are_here").find('.item').each(function( index ) {
     var item = $(this);
     setTimeout(function(index) {
            $("#container").isotope( 'insert', $(this))
     },index*3000);
    });