For brand new parts, RHD Japan are awesome. Can get parts over here in a few days as well if needed (at a price of course)
For auctions it's a bit of a weird one. I've used Jauce before and where it's really good in being totally in English you're required to bid etc yourself (not always brilliant with Japanese time differences)
I tried them out with a simple purchase 1st, a set of JDM EP3 floor mats. I won the auction for something stupid like £20. But once you add on their auctions fees, the domestic and international shipping I think it cost me nearly £90!! So not much cheaper than a set already here in the UK.
A few of my mates have used a guy/company called Jesse Streeter. The good thing is that he is an American based in Japan and can speak both Japanese and English.
So you browse the auctions, find a product you want and send him over the link. He will translate it into English for you and highlight if there are any problems etc. As he is based in Japan he will also bid on it for you to whatever your limit is and can provide a good guess at estimated shipping prices (the vast majority of people in Japan won't post outside of Japan so they block overseas bidders).
If you want wheels, they will also remove the tyres for you (something Jauce won't do). Generally I find it a bit more reassuring that you have someone at the other end to communicate with before bidding and potentially getting a set of cracked wheels for example.