I've only ever used ShoppingMallJapan, but I have not been doing so very long... (well, since 2009 but maybe only since the summer I think?) like Maraviollantes describes with japamart, you put in a deposit but it can take awhile for the deposit to come through... however they convert your deposit to yen and then they basically give you bidding power up to 5X that amount... so I think I have only given them a $50 deposit, which could roughly translate to 5000 yen, but I am able to bid up to 27500 *something like that* I'm not sure how it works on other bidding sites... but it is nice that they allow more... but I did only start with a $25 deposit, and annoyinggly found it too low for me to bid up multiple auctions, since I would maybe want to pay 5000 yen for three different ones *thus 15000 yean total* but could only bid up to 12500 which is a problem when you're trying to win all three ^^; although it is automated bidding now which is very nice. They also have "manual bidding" which from what I read is to be used for if you want to do BIN or Adult themed stuff I guess... I've never tried it.
However, there are glitches in their system... the other day I had the worst one... I had been bidding on a plush set but it started going for an insane amount... so instead of focusing my bidding on it I decided I wanted to try for a wand... but the bidding system glitched and even though teh auction was much higher than my bid, SMJ still read me as "winning" and so my money was held for that item, and I was not able to bid on the other one ending. So I lost a few auctions I could have bid on. This was my first real time having an issue with SMJ though...
Like someone else said, it is easy to overbid/buy b/c of their leniency on how soon you have to pay haha... I also love that their sorting facility in the US is in IN so I will sometimes get the item before the shipping invoice

Since they ship the items and then send you the invoice, so that it's for the exact amount of shipping...
However, it also can take awhile for items to even get batched to the US... I had some items already nearly a week old getting sent to the US. BUT they do combine shipping, and will even hold your items for about a month before they charge you any storage fees. They don't ship to your home from the US office until you tell them to. Unless the item is supposedly cheaper to be sent straight from Japan *had that happen once, and it cost me $60 to ship!

T_T*
Overall I like SMJ, they seem very nice and he fact that in the US it's stored in IN makes shipping within the US super cheap and fast for me!! It's one reason why I don't want to change ^^; as for their commission fees, I don't know how they stack up against others.. I know it goes by increments, something like $5 for auctions from 1-2500yen or sth like that... sometimes it's a bummer ^^; Remember that the exchange rate also plays a factor... right now the yen is a little stronger than the US $ *has been for awhile* but once the US $ dipped and I had two auctions same price but a few days apart, and I ended up paying more for one ^^;
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As to searches, when I go to Yahoo Japan Auctions I have a bookmarked page with "セーラームーン” already in the search field... so the page automatically brings up SM auctions... from there since I know some Japanese I find it's not to hard to search if I go for specifics... but also if you click on the search field, type a space after it will *like eBay* give you options of common searches like "セーラームーン コスプレ” (Sailor Moon Cosplay) so that helps, too. I've never used SMJ's built in search engine...
If I really need help knowing about an item I usually put it in Yahoo's Babelfish translator... it's usually a pretty weird/bad looking translation, but I can get some of the more important info like whether they tested the item (like a wand) to see if it works... but it will say weird stuff like "There are also some which is not the cover of the part which inserts the electric battery." -Seriously, I just took this from an auction's translation ^^; It means that some are missing battery covers... but it is a weird translation as you see...
Anyway, sorry to talk so much but I thought I'd offer my little bit on SMJ... it has good and bad points but overall they ship items very securely and I don't think the wait is too bad... I mean, it takes 2 weeks to send something to Germany straight from my home. I can sometimes get an item that had to go through two shipping services/get invoices and pay them/be combined with other auction buys sometimes in about the same time frame if I win the items within a day or so of each other...