(Review Structure stolen off Cidsa. I hope she doesn't mind!!)
Shopping Mall Japan http://shoppingmalljapan.com/Yahoo! Japan: Is all yours. You sign up with them, and place a deposit. Depending on HOW you send your deposit, you can receive up to 5 times that amount. IE. A 5000yen deposit paid via paypal will receive a bidding limit of 25000yen. Then you login, and can view your bidding limits, as well as current bids. As for bidding, you do your own, which is fantastic for those Last minute bargains. [Well, as last minute as you can get on Y!J]
Online Stores: You need a active bidding limit of 10,000yen or more. A bit silly if you want a 500yen toy or something, but fantastic for those more expensive items. $5.00 fee is charge to place the order itself,
WHETHER ACCEPTED OR NOT. $2.00 for each additional item. This is ONTOP of the normal fees.
You simply fill out a form with the details of the item and wait until they reply.
Fees: The fees seem rather good, however, once you add internal shipping and bank transfer fees, prices can get a bit steep. Especially if you bid/order more than one item. Fees tend to pile up. *looks at her own list of items*
Payment: Payment is expected within 14 days, but if you have some problems, just email SMJ. They are always very generous.
The money in your deposit/Active Bidding Amount does not apply to your grand total at the end of an auction, UNLESS you request a specific amount be removed. Please don't forget your giant bidding amount isn't actually that..but just a 1/5th of.

" SMJ Take Paypal, Check, Visa, Discover and Money Orders. You get invoiced a few days after the auction with a price breakdown.
Shipping: SMJ do not notify you of an item's arrival. You must check it for yourself on your userinfo page. You can request shipping whenever you want, and for whichever items. The fantastic thing is, i've had items with SMJ for nearly two months, just to save on shipping at the end. EMS, Priority, Parcel, Standard Air and Surface Mail services are all offered. Fill out the 'request shipping' form, and choose a method. You will be invoiced within 3 days.
Customer Service: Customer Service is great. Questions are answered promptly and very nicely, and Nick over there was always so helpful when i was a n00b and deleted my own password accidentally.

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Overall: Fantastic, but beware how the fees can pile up if you're not careful. Real Time bidding is an extra plus! I'd recommend SMJ for auctions, but not for online stores.