The mint.com of Japan
It's basically the closest thing to mint.com for the Japanese market that I have found so far.
The best thing about the free app is that it categorizes things automatically, learning from your usage patterns.
You can enter cash transactions manually, and it will track credit card spending by category automatically.
I use several different credit cards (mainly for air miles and hotel points) so find the tracking invaluable to make sure I have enough cash on hand for the monthly withdrawals.
If you trust the company with your login information, and they seem to be getting big enough for that to be less of a worry, this is a wonderful personal finance tool.
Are there any other good personal finance trackers for Japan?