I flew A340-600 on HKG-FRA and also got upgraded to PE once on 747-8 FRA-HKG. The PE seats are basically the same on the two aircraft but I feel A346 slightly quieter (perhaps because I was at exit row on 747-8).
I would say that PE gives me larger seats and nice touch here and there (e.g. amenity kit, pre-flight drink, bottle of water). If it is a day flight and I know I will be watching movies throughout the flight then I might save the money, but for overnight flights I would definitely pay more for the comfort to get a good sleep.