Taxis 
picture courtesy of online tomodachi
In Japan, where trains stop running around midnight, taxis are the only alternative available if you want to get home in the middle of the night. Also, if you don’t feel like figuring out where exactly your stayover place is, having a taxi driver find out for you can be much more relaxed.
Taxis in Japan are generally very reliable. They are not known for scamming customers or driving especially around to drive up the price. There are a few things to keep in mind when using a taxi though.
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Again, they often don’t speak English. I’ve been in taxis where I suspected the driver to have experienced WWII, so many of those will have no idea what you mean if you don’t speak Japanese. The best trick is to take a business card of the hotel with you, or ask someone to write down the address of the apartment in Japanese so you can show it to the driver. Problem solved.
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Don’t try and open the door. This is a well-known first-timer mistake, but taxis in Japan have automated doors that swing open upon approach, so you don’t have to do all that work yourself. Note too, that only the left doors (seen from when you’re inside) open, so you have to scoot over once getting in. This is to prevent open-door-car-accidents.
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Like in restaurants, it is not customary to tip.
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If you want to tour around an area with limited public transport for a whole day, or for instance you have someone with you that has a poor walking condition, hiring a taxi for the whole day is also an option. Check for instance http://www.car-jtsa.com/english/rent-a-car-user-s-guide/ around Tokyo, or http://www.mktaxi-japan.com/ around Kyoto and Tokyo.