I'm surprised nobody has mentioned "From Japan" yet.
Lowest fees I've found. 200 yen + 5%, always. There's also the 5% bank fee though. All services have this although some hide the information well.
So for a 5000 yen item, you'll end up paying 5913 yen, while it's typically 6353 and up if you use another service.
I've been using them for two years now and they have been great.
There is also a promotion until the end of the month now, so if you register through this referral link and buy something, you'll get 1000 yen to spend on your next order. It's not that much though, but always something.
http://www.fromjapan.co.jp?afid=N97102
(The whole url didn't turn into a link, so you would have to copy-paste)
They also have 5% off campaigns quite often. This applies both to auctions and regular shopping.