The site used by most Japanese people, and hands down the most popular is called CookPad. There is even an iPhone app for it... the recipes are incredible ranging from traditional Japanese foods to American, Indian, Italian, French., anything you can imagine.
The site is in Japanese.
(If you don't read Japanese, there are currently three menu selections at the top. The one on the left is "Welcome". The middle one is "Recipes", and the last one is "Submit", to submit a recipe.)
Google translate works pretty well with this site!