Many of the tourist sites we saw in Japan were Shinto shrines or Buddhist temples. Japan has the, to western sensibilities, odd situation in which most people adhere to two religions. People go to Shinto shrines for happy events, such as births and weddings, but Buddhist temples for sad ones such as funerals. This state of affairs seems to have come about because Shinto worship consists entirely of venerating local deities; there's no code of ethics around which to structure one's life, and Theraveda Buddhism appears to have moved in to fill that gap.
This state of affairs with regard to Shintoism also means the religion has no holy books, which made aviva_m question where the rituals that we saw came from, then. Presumably they were all transmitted through oral tradition.
Actually, most people in Japan today are fairly secular (this may be because some of the great Buddhist temple complexes supported revolts against the shogunal government a few centuries ago, and the shogun responded by breaking their power in the land). Quite a few, seeing western-style church weddings in films, decide they want one themselves, so join a church a few weeks before their wedding in order to be able to achieve this—leading to the crazy situation of their having three religions at once.
Shinto shrines are to be distinguished from Buddhist temples in two ways. One is that before making an invocation to the enshrined deity, one claps one's hands twice, presumably to get the deity's attention, then bows; the other is that the approach to every Shinto shrine is marked by the presence of at least one Torii gate, usually, though not always, of red-painted wood, marking this as holy ground.
At the start of our holiday, Andrea and I spent a few days recovering from the jet lag in the beach resort of Atami, less than fifty miles from Tokyo. There we encountered our first shrine, called Kinomiya Jinja.
It is the practice to wash one's hands and mouth before making an invocation at holy sites—something my Jewish readers will be very familiar with. Here's some כֵּלֵי נְטִילַּת יָדָיִם I photographed at a shrine elsewhere.
Also common with Judaism was a ban on taking photos of services, so we have none of those; instead, just lots of ritual objects we didn't really understand. This I think is either where the deity is enshrined, or a portable shrine in which the deity can be removed from the main shrine on religious occasions which demand it. (Note: This photo is coming out upside-down for me, despite my best attempts to fix this, on Firefox, Safari and Chromium, but if you click through to see it full resolution, it displays the correct way up. Computers!)
Here's a video I found on YouTube of Kinomiya, including rituals being performed there. In the meantime, have some koi:
This sequence of torii gates is suggestive, but only slightly, of the Fushimi Inari shrine in Kyoto, apparently Japan's number one tourist destination, where there are ten thousand torii gates in a row, but which we visited on Shabbos afternoon, so we have no pictures of it. Here's khiemtran's report of his trip to Fushimi Inari, which was what made me want to visit there in the first place; or alternatively, you can look at some photos on the Wikipedia page.
You'll be getting to see plenty more shrines and temples here in due course.