The big difference between European and Japanese trains are that Japanese trains have reserved cars and non-reserved cars. Passengers without seat reservations cannot sit inside the reserved cars, even no one made the seat reservation for that seats.
Normally in Europe, trains are either compulsory reservation or non-compulsory reservation. Then, trains with non-compulsory reservation can be either you can make a seat reservation or seat reservation is not possible at all.
Some of the Japanese trains have compulsory reservation system. Hayabusa trains of Tohoku Shinkansen, Kagayaki of Hokuriku Shinkansen, limited express Tokiwa, Hitachi, and Narita Express are the major trains which have compulsory reservation.
Normal passengers must pay an extra fee for seat reservation but Japan Rail Pass holders not. Japan Rail Pass holders can make seat reservations for free and I strongly recommend to make it for following trains.
1) Sanyo Shinkansen Sakura trains between Shin-Osaka and Hakata(Fukuoka)
2) Limited express Azusa(Shinjuku-Matsumoto)
3) Limited express Thunderbird(Osaka-Kyoto-Kanazawa)
4) Limited express Hida(Nagoya-Takayama)
5) Limited express Kamome (Hakata-Nagasaki)
6) Tohoku Shinkansen Yamabiko/Hayate trains between Tokyo and Sendai
7) Limited express Super Ozora(Sapporo-Kushiro)
8) Rapid Mie between Nagoya and Ise-shi
9) Rapid Marine liner(Okayama-Takamatsu)
Also, Hikari trains of Tokaido & Sanyo Shinkansen have only 5 non-reserved cars out of 16 cars. On the other hand JR Kyushu has several limited expresses which have only non-reserved cars.