What is the best website for booking overnight trains in Western Europe?
It depends where. If it's overnight train from Denmark to northern Sweden then Danish or Swedish rail website. If from France to Spain then Spanish or French one and so on.
I booked both of my night trains for this spring, Amsterdam to Munich and Munich to Venice, on http://www.bahn.de/
Jeremy booked his trains on Deutsche Bahn website because one of his trains went to Germany and other one started from Germany. If your train let's say goes from France to Spain you obviously cannot book it on German railroad website (Deutsche Bahn) but it would have to be French or Spanish railroad website.
Not a booking site, but the best place to get answers to train booking questions: www.seat61.com Search The Man in Seat 61 for the city you will depart from. Pick your destination city on that pag3, and he'll tell you how book the train.