I've lived in Japan before, and with a Japanese family, to boot. So, sometimes I feel like I have a little more insight than the average bear. I started thinking about some of the most important things for people to take into consideration during their trip to Japan and I made a list:
Learn to bow and say excuse me. - I think that すみません is my most uttered Japanese word. As far as bowing, it will start to become a habit. You will bow while talking on the phone, and you will bow if someone lets you cross the street & there is no walk signal. Even a slight nod is a sign of 'I respect you' and it puts people at ease.
Learn some Japanese. - Even a few words go a long way. People really appreciate it when you try, and it makes a lot of Japanese people who don't speak English feel so much more comfortable with you. And don't just prattle off the titles of your favorite manga/anime in Japanese. Learn to ask where things are, get directions, how to count money, and what the server suggests on the menu (お勧めは何でしょうか？）
Eat the food. - Yeah. I know. Japanese food can be really weird sometimes (natto, umeboshi, uni, basashi, just to name a few) but trust me, despite looking super strange, you might just find something you really like. At least you can say that you've tried it. Plus, it is really polite to finish your plate, double points for that!
Don't question everything so much - sometimes it's just best to accept things for the way they are and deal.
If you go to a shrine or a temple, be sure to take photos in appropriate places - yeah. Sometimes people get really offended if you take pictures at religious venues. If you NEED a photo, try to be discreet, ok? Unless of course everyone else is taking pictures, too.
What may seem strange to you, might not seem strange to someone who's lived in Japan their whole life. - Example: the Japanese variation on English. There was a Hair salon not far from my host family's house, but instead of saying Hair Salon on the storefront, it said "HEAR SALON." They caught wise when they saw the gaijin standing outside and laughing. They actually changed the sign in the next couple of days. How's that for saving face?!
Sort your trash - just do it. It's good for the planet and your neighbors won't hate you.
Bring something to read that is written in your native language - sometimes listening and reading to Japanese all day makes me really tired... and I need some English time.
Go to Hiroshima. Visit the museum and the monuments. Be respectful.
Get to know the town where you're living - you never know there might just be something really awesome about it that you never knew. Hirakata, where I used to live, was famous for its yearly chrysanthemum festival. Two stops up on the train line was a shrine to Thomas A. Edison!!
Take the Shinkansen somewhere at least once - Especially if you're living on a student budget, shinkansen tix can be kind of expensive. I love the bullet train, I wish they had them in the United States.
Start walking and biking - unless you've got a car, you are going to need to kick up your walking/biking skills a notch. Japan is all about those two modes of transport!
Watch SOME Japanese TV - come on, even if you don't understand it, its just ridiculous and entertaining. The commericals are great, too.
Don't get upset if they don't have your size - Man, I really wanted so many adorable Japanese clothes, but they never had the sizes to fit my gigantic American frame. I found some cool accessories to wear w/ my American digs, but don't fret, while you may feel that you look dumpy and gross compared to the super-amazingly-put-together-outfits of Japanese women, some of them secretly envy the comfort of your chuck taylors and inexpensive jeans.
Make sure you have enough cash - Yeah.. lots of places DO take visa, and some even take Amex, but in a lot of little towns and out-of-the-way shops/restaurants they only deal in cash. Postal Service ATMs are super convenient.
Don't let the culture shock get you down - yeah, I've been denied service at restaurants and turned away when I needed to do important things like get a cell phone, but don't let it get you down. It's not that they don't like you... it's kind of an irrational fear of someone so different, and not being able to help you properly, ne?