Japan Cupid has connected thousands of Japanese singles with their matches from around the world, making it one of the most trusted Japanese dating sites.
It does, however, filter by race and your desired race(s) to date, so it's a hard one to beat for the sheer number of users.
Even today, only a small fraction of the population has signed up to an online dating site as most Japanese believe it is more acceptable to meet potential mates via the traditional methods of mutual friends, organizations, work, school, etc.
However, I do believe this will change and internet dating will become more mainstream with time.
Unless otherwise mentioned, each site expressly supports interracial relationships, and I'll note where they also support LGBTQ relationships, polyamory, and/or focus entirely on marriage-minded singles.
Asian Date Net (formerly on this list as Asia Funs) offers more than the standard set, such as dating blogs, couples dating, and news, they also offer a fun constantly-changing ticker along the bottom of the main page, showing who logged in last and a few details about them.