Mandrake's
Nice page, I liked it a lot because they had a huuuuge list of rock/metal bands... lately, they are more into Visual Kei, but you will find a lot of surprises there (believe me)
Disk Union
Amazing site to find stuff in Japan, they even have special stores for different kind of music... highly recommended, I usually buy some punk stuff here (when I'm not into trades, hehehe)
I hope this sites be helpful for all of you, who are tired of the same sites, hahahaha ^^
Yesasia is good but its search function isn't that great and its product availability and list isn't as good as hmv.co.jp.
Cdjapan has a nice selection, but the shipping costs are high, not having the free super savings option of yesasia.
I haven't tried hmv.co.jp, but it looks like they have more products available, or at least listed. But they only accept credit cards. They don't even accept IPMO...