var firstDate = '23.09.2016 22:20';
var secondDate = '01.10.2016 00:00';
var datetime_regex = /(\d\d)\.(\d\d)\.(\d\d\d\d)\s(\d\d):(\d\d)/;
var first_date_arr = datetime_regex.exec(firstDate);
var first_datetime = new Date(first_date_arr[3], first_date_arr[2], first_date_arr[1], first_date_arr[4], first_date_arr[5]);
var second_date_arr = datetime_regex.exec(secondDate);
var second_datetime = new Date(second_date_arr[3], second_date_arr[2], second_date_arr[1], second_date_arr[4], second_date_arr[5]);
if(first_datetime.getTime() > second_datetime.getTime()) {
console.log('первая дата больше');
} else {
console.log('вторая дата больше или даты равны');
}