Having been lucky enough to fly long range on the 777, 747, A346, A332, A388, 787 and A359, I can confirm that flights on the last two types were much much comfortable than on the first five types.
I do remember when getting out of the A/C after our first flight on an A359 (MUC to YVR - 10 hours), both my wife and I said at the same time "it's quite surprising;: I am not tired as usual !".
No miracle on that: tdtracer is fully right in mentioning the 8000 feet (777, 747, A346, A332, A388) vs the 6000 feet (787, A359) cabin altitude as the main reason for the feeling of comfort.
When possible (and ticket price permitting of course), I now privilege 787 and A359 when booking long range flights.