Try this:
var array1 = [1, 2, 3, 4, 5, 6],
array2 = [1, 2, 3, 4, 5, 6, 7, 8, 9];
var common = $.grep(array1, function(element) {
return $.inArray(element, array2 ) !== -1;
});
console.log(common); // returns [1, 2, 3, 4, 5, 6];
var array3 = array2.filter(function(obj) { return array1.indexOf(obj) == -1; });
// returns [7,8,9];