1. There are 4 kinds of seating cars on a Shinkansen: Reserved Smoking, Reserved Non-Smoking, Non-Reserved Smoking, and Non-Reserved Non-Smoking. Be sure you know which car you're getting into and which type of seat you're getting, if you make reservations.
2. Shinkansen non-smoking, non-reserved cars are usually cars 1 & 2.
3. I recommend getting to the Shinkansen platform at least 20 minutes early if you don't have reserved seats; lines form. During major holidays (Golden Week, etc.) get there as early as possible; the lines will be in the news.
4. Since Tokyo is the beginning of the line, getting there early really does make a difference for non-reserved seats.
5. Traveling between Osaka and Kyoto, you may not be able to find a non-reserved seat and may have to stand. Non-reserved seating tends to be more difficult in the Kinki area, in general, but I've had problems from many of the stops between Kyūshyū and Osaka.
6. If you do have to stand, try to avoid standing in front of the doors or you may be forced to exit the train at the next stop. If this happens, just stand to the side of the doors until the people exiting are all off, then get back on in front of the other people waiting to get in.
7. Shinkansen are different lengths, so be careful of the car number when waiting. And remember—from Tokyo, blue Shinkansen go south, green Shinkansen go north.
8. The front of car 1 is the best place to avoid smoke on Shinkansen. Feel free to ask anyone smoking in or between non-smoking cars to stop. You're a gaijin; you can get away with it.
This is a non-smoking car.
Kore wa kinensha desu.
Please don't smoke.
(Tabako o) suwanaide kudasai. or
Kore wa kinensha desu ga... (tabako o) suwanaide kudasai.
You can begin any of these sentences with “Sumimasen,” if you want to be more polite.
9. If you have a JR rail pass and want a reserved seat on the Shinkansen, you'll have to pay extra to get one. JR rail passes are invalid for tickets on the newest, fastest Shinkansen, the MAX and Nozomi; expect to pay big bucks to ride one.
10. Try to bring your own food. The food you can buy from vendors and in dining cars tends to be really expensive, though it's kind of fun to eat in the dining car (their corn soup and a roll was affordable). And I must mention that the food in the platform bento shops on the Tokyo station Shinkansen platforms is very good.