I really liked traveling in Japanese long-distance trains. In addition to the stuff I wrote about earlier, two more points occurred to me during my last trip in Japan.
First, the leg space you get is enormous compared to planes, or even German trains. Not that the average Japanese person needs a lot of leg space... but I thought it was very nice and relaxing.
And second, I like the way the seat reservations work. In each train, there is a designated number of cars for non-reserved seats. All other cars are for reserved seats only. So if you have a reserved seat, there won't be other passengers roaming about in your compartment looking for a free seat. And if you don't, you know which cars you can find a seat in - and don't have to search the entire train if these cars are full. By the way, I've always found a seat in the non-reserved cars.
Back in Germany, I was immediately reminded that German trains are not as punctual as the Japanese ones. During my second train ride, I was waiting in the train at one station, when there was an announcement on the speakers: the train's departure would be delayed indefinitely due to missing train personnel. Well, "indefinitely" turned out to be just a couple of minutes, but I thought that "missing train personnel" was a hilarious excuse for accumulating delay. Stuff like that just doesn't happen in Japan...