First, you must know that there are different types of temples. The two main categories are the family-run temples serving and attached to a graveyard for a small community and the major touristic ones.
Most main temples have the same temple layout. Smaller ones commonly have more than 3 buildings.
A small family-run temple will look like this:
This temple, like so many others is not meant to be visited except by people who have family graves on the grounds. This particular temple is in a small town called Kainan, in Wakayama prefecture.
It is right next to where I worked. These temples are easy to spot. First they are the most common temples in Japan. Of modest size; they often have a gate that is closed at night. On the grounds there usually is both a house and a hondo (worship hall). There are usually several gravestones and very rarely a basin for purification at the entrance.
You are still welcome to enter the grounds but the hondo is usually closed and you only have access to the graveyard. It is for families to tend to the graves.
The other type is the more touristic one: we can enter the grounds, visit the hondo and even worship in some areas. Many have activites related to the teaching of Buddhism. Some of them also have important cultural assets that you can see.
The "touristic" temples, come in two types: the smaller ones who are free and the more important ones requiring a contribution ranging from 100 to 500 yen to enter. (Between 1$ and 5$)
The pricier ones usually are ancient and contain important statues, art or other cultural assets. The contribution allows for maintaining the building, paying wages and saving for rainy days.
Above, you can see the main hall of Todai-ji in Nara. It shelters the Great Buddha. At the time of writing this, the entrance fee to the compound is 500 Yen. It is the biggest wooden structure in the world and has thousands of visitors every day.
I am sometimes asked by people what to do when at a temple. For foreigners it is a mystery as for most of us, temples are not part of our culture. The etiquette is quite different than what we are accustomed to in churches.
Here is a list of some important Japanese temples in Japan with directions and what you can do once there.