The traditions that foreigners don’t know?

When foreigners arrive to Japan, what are the most important traditions/etiquette rules they should be aware of? I already know that the japanese are tolerant to gaijins, but a little knowledge wouldn't hurt.

Are tolerant??? Hummmmm....

Maybe you meant "forgiving" when you said "tolerant"?

At least check this page out....

http://www.japan-guide.com/e/e622.html

yup, meant forgiving. I know that the ones "seeking" contact with foreigners are more open-minded than others. And I already read that page, but I'm not just gonna step into the country, morph into one of them and start using all those habits.

My question remains, which of these traditions are the most common/stand out and are best to be taken into consideration.

which of these traditions are the most common/stand out and are best to be taken into consideration.

Well, all of them are equally common and are best to be taken into consideration.

Again, no one, including those who don't "seek contact" with foreigners would mind mistakes made by tourists just passing by.

But just as you'd do in any country, look around for signs or guidances for tourists or locals to learn from. And if you remember reading something but are not sure what it was, just ask.

If you're going to live here, people will expect you to follow all the rules, so talk to your landlord and guarantor well.

If you happen to be scared of making any mistakes at all, stay at a western style hotel and stick to what your accustomed to. But that would be a pity, wouldn't it.

1. Don't be loud.
2. When passing a threshold, always look down to see if you need to change shoes. ;)

In addition to above plus etiquette page:
3. Don't eat or drink when walking.
4. Don't eat or drink on a commuter train or subway (Shinkansen or JR limited express ok).
5. Separate garbage into correct bins or carry in pocket if no trashcan
6. Don't talk on your 'phone on trains and don't use at all in designated areas by priority seats
7. Don't smoke and walk and only smoke in designated places
8. Don't cross road on red man
9. Stand/walk on correct side of the escalator

You will see Japanese break all these "rules" - except 2. the shoes one

10.- not a tradition/etiquette, but the law: carry your passport with you at all times

Don't eat or drink on a commuter train or subway

Hmm... my grandma and I shared a small drink on commuter train, and we're Japanese.... but we weren't exactly gulping it down, though. More like little sips.

Ever since I came to Japan for the first time, I have wondered, why you must turn your mobile phone off when you are near the prioity seats? I mean why isn't the silent mode enough, like in other parts of the train, what's the point? Of course Isee everyone breaking this rule all the time..

@tolkkizz
They said the radio wave of mobile phone have harmful influence on somebody using artificial/cardiac pacemaker.
I heard mobile phones have no influence on pacemaker over 22cm.
http://www.soumu.go.jp/menu_news/s-news/02kiban16_02000032.html