30 useful tips for travel in Japan

Prayer in Japan
Japan is said to be a land of “many gods” – and is hence dotted with many Shinto shrines and Buddhist temples. Religion for the most part is customary in Japan, not is necessarily a major part of everyday life for most. Funerals, for example, will involve either Buddhist or Shinto practice, depending on the family.
Shintoism and Buddhism, shrine and temple
Shintoism is the “native” religion of Japan while Buddhism is an import from abroad that has been adopted into Japanese culture. In modern Japan, many funerals are handled by Buddhist institutions. Buddhism has monks, who often have shaved heads and wear robes of varying colors - orange and purple being the most common. Buddhist temples are not usually places for offering prayers for good luck, but are rather for meditation as well as remembering one's ancestors since family tombs are located near such temples.

Shinto shrines, on the other hand, are more for visiting casually and making a prayer. They are very easy to spot as they have “Torii” arches. The wooden structures (many of which are painted red) are supposedly the entrances to the gods' territory, and therefore one should walk near the left or right edges rather than go walking in the middle. They also have bells and an offering box after the entry point. Before going to make one's offerings, one is expected to cleanse oneself. There is a water “fountain” area with ladles; you should pick up the ladle, wash one hand, then the other, before washing your mouth (but don't gargle!). Then, use the ladle to wash the handle portion by letting water down from the ladle cup by holding it vertical. Again, watch how the Japanese visitors conduct themselves at the “fountain” area and act accordingly.
How to Pray
After cleansing, go up the steps to the offerings area, First, make your monetary offering into the box (just coins are fine, with the five-yen coin thought to bring greater luck), and sound the bell if there is one. Following this, there is a special routine for praying at a shrine. It is easy to think of it as "two-two-one". Two bows, two claps, and one final bow. First, bow twice to initiate the prayer routine. Following the two bows, clap your hands twice (the hands are not clasped, but shaped as a steeple). This is when you make your prayer silently to yourself. Finally, bow once more and calmly leave the offering area. At a temple, place a candle or incense in the designated place, throw in a coin, and join your hands in prayer silently. Do not clap your hands. Other visitors will be doing this routine as well. If you want to see how it's done, observe first before trying for yourself.