Personally I use Anime Jungle.
You can find new and used CDs/DVDs/merchandise there and the prices and quality on the used items are amazing. I've bought CDs from them many times at 1/2 to 1/3 the price of the brand new copies and they look brand new even though they were used! (I actually e-mailed them to verify they were used.)
http://jungle-scs.co.jp/cgi-bin/cart_e.cgi
Sometimes it's a bit hard to find CD singles though if you aren't looking for something specific or a 3 inch CD single since they put all the Maxi Singles in with the normal CDs. But searching through all the pages in that case can be worth it sometimes since you can find really rare CDs.