Traditional Japanese toilets are still common in public bathrooms and some homes.
They are a trench shaped hole with a drain at one end.
To use one we need to squat with a foot either side of the trench facing the direction of the hole.
The rest is natural and will be evident

Modern Japanese toilets are super advanced and computerised and you can see all about them by looking at this video:
http://www.metacafe.com/watch/539639/toilet_computer_operated/

If you want to know more about this delicate subject or want to share your experiences (do we really want to hear them?? ) please post here:

UPDATE!

woah..it's been two years! *haha* ii would like to share about toilets too. They are pretty clean everywhere..However, I never been to the public toilet yet.

The Traditional/Old-fashioned Toilet:



The Modern Toilet: When you open the door, the lid will automatically open for you. And it has a function of auto-flush (if you're being lazy) after 1-minute standing infront of the toilet seat. Then, there's buttons for you to lift up/close the lids or the seat-thingy. The type is similar as shown by the OldDude. Most toilets in Japan are now westernized for both Japanese & Gaijin comfort. Another best part, if you dont use the toilet anymore and you walked away. The toilet will half-flush itself again & automatically close the lid! Awesome!





The Modern Toilet's Instructions:



Typical CHILDREN toilet - Shared (Male/Female)It's amazing to see these cute little toilets made for the children. This toilets are usuaully found in kindergarten/nursery schools.