Here are some random thoughts and tips that might not be obvious to first-time travelers to Japan. I'll throw them in as I think of them, so they may not be in any particular order...
Lockers are an awesome invention you can find at most train stations and there are even bigger ones at larger stations. I'll even use them for stuff like leaving my work bag in there after work so I can travel light while hanging out w/friends or leaving big shopping bags there while we keep shopping or eating. Many at older/smaller stations may still use 100 yen/500 yen coins, but the newer ones are IC-equipped, so make sure you have your own PASMO/Suica!
Random tips:
- Look up! Coming from relatively flat cities, it took me awhile consider that there were other business/restaurants above ground level! Depending on the building there could be great places on the 10th floor or even 50th! Many of the restaurants and shops will be perched up in tall buildings and if you're feeling adventurous, you'll miss them if you don't check out the signage. Of course, your mileage may vary if you can't read Japanese, but at ground level there are typically signs on the building which show more info about the shops above.
- Ordering at a coin-op machines for restaurants is not a sign of cheap/bad food! I believe some of the best ramen (perhaps one of the Michelin starred ones?) uses a machine where you put in money, select your order, then you get a ticket that you hand to the people inside. You'll see this often at ramen (or other noodle) and curry/rice places. It makes it easy to get in/out. What's nice about these kinds of places is that even if you can't read Japanese, often there are "fake food" samples or pictures outside that list the menu item. So you can just match up what's on the picture, with the button on the machine!
- Shoes are dirty (obviously!) so don't put your feet up w/shoes on another chair, bench, train seat, etc.
- Trains have special seats for older/pregnant/disabled folks which are marked, so please leave them open or get up and give your seat to those in need!
- Escalators! In Tokyo, you stand on the left and let people walk on the right. Any exceptions to this would be marked or you'll just see the people. In Osaka, it's opposite! In Kyoto, it's either - just do what they do - they're not in as big of a hurry as Tokyo-ites
- Depa-chika - Department Stores have awesome grocery stores in the basements - definitely worth checking out for supplies or for food/pastries to take away (to eat at hotel or on a trip). Depa-chika comes Department Store and down/below
- Convenience stores are everywhere and have tons of stuff that you may need, including a dizzying array of drinks/snacks/food and some larger ones even have a microwave and seating area
- If you don't see what you need there, you may need to check out a proper "pharmacy" store like Matsumoto Kiyoshi (yellow sign - easy to spot) - one example was diapers for our daughter when United lost our luggage for two days...
- Don't eat/drink on the train! No one really wants to smell your food or risk having it spilled on them
- Take advantage of your hotel's concierge - if your local friend doesn't have restaurant recommendations for you, they can help you make reservations; there are plenty of good restaurants in the stations as well! Some are obviously fast-foody, but many are legitimately good and can have long waits