You will find Japan to have some of the best service in the world; however, tipping is frowned upon.
Cash versus Credit Cards
¥100 ≈ $1
Cash is much more common in Japan than many other countries. Ensure you have a decent amount of Yen in the event that an establishment doesn’t take credit cards.
Remove Your Shoes Inside
It is extremely common that you will need to take your shoes off when entering certain places in Japan — e.g., homes, traditional restaurants, inns, hot spring buildings. This is a very important protocol of which to be aware.
If you enter a space and see a small step right inside, this is a strong cue that shoes must be taken off. If you see shoes already placed just before the step, or you see slippers on the step, these are additional cues to remove your shoes.
Take your shoes off before stepping up; do not step up with your shoes on or place them on the upper step. Either leave them in the lower entrance way, or sometimes there is a rack to the side to place your shoes.
Tip: Wear slip-on shoes. Shoes or boots with lots of laces will quickly become annoying when you have to take them on and off many times a day.
You will likely not take a taxi, but if you do, one thing of note is that you don’t actually open or close the door. The driver has a special lever that opens and closes the back door, so let him do it.
You will notice "Seven-Eleven" ("7/11”), “Lawson”, “Family Mart”, etc stores all over Japan. These convenience stores (“kon-bi-nya”) are much better than what you are used to in the US, and the pricing is not much different than a regular store. Japanese rely on “konbinya” on a daily basis, so don’t shy away from frequenting them. They are also a good place to access ATMs, too.
Please enjoy Japanese toilets! These are called “washlets”, the heated seats, automated bidet, and butt cleaning features are awesome. They are a bit intimidating at first, especially if the controls are Japanese-language-only, but usually there is some sort of pictogram to help out.
Smoking is fairly prevalent in Japan. Most restaurants, bars, and cafes allow smoking. These establishments often have “non-smoking sections”, but these are typically very small and poorly isolated from smokers.
Do not hesitate to eat / shop at train stations in Japan. There are lots of excellent restaurants right in many Japanese stations. Tokyo Station, which is sort of like New York City's Penn or Grand Central, has innumerable dining establishments. So, don’t feel like a restaurant is sub-par because it is in a train station; in fact, some of the better ones are in stations because of the proximity to people. I believe some michelin-starred restaurants are in Japanese train stations, and I’ve had plenty of amazing sushi and ramen in train stations.
Grocery Store Sushi
If you are feeling a bit overwhelmed trying to find places to eat, then don’t hesitate to grab food at a local grocery store. In particular, the fish sections of most stores are stocked with excellent cut sashimi and sushi rolls at an affordable price. The nice thing is that, while you might not be able to make out the exact type of fish, you’ll be able to see the general look, quantity, and price. While I eat sushi at restaurants in Japan, it is not uncommon for me to pick up sashimi at a nearby grocery store, since it is much less expensive and excellent. Same can be said for a lot of stuff in Japanese grocery stores; so, again, don’t hesitate to pop in and turn something into a meal to avoid the stress of trying to figure out a menu at a restaurant.