eBay never got off the ground here. Sellers enjoy the concept of a site that has no fee for listings - eBay has listing fees, final value fees, PayPal requirements and fees. And all those happen for every auction. Yahoo started with no fees at all, though they now charge a monthly fee (about $4) and a flat fee of about 5% on final auction values (with some exceptions), also seemingly calculated monthly.
Another problem I think eBay had was payment methods. Japan relies heavily on bank transfers, and the heavy emphasis on PayPal really made things tough. Yahoo does have an online payment system where buyers can pay with credit card or bank transfers through their site, but bank payments are still allowed.
Yahoo in Japan feels a lot like eBay did when it was great - relatively simple and fairly user-friendly if you understand Japanese. I usually use the website, but the iPhone app is pretty handy too. The low fees for sellers means prices start fairly low and shipping is via post - 82 cents at the lowest.
Now, paying for auctions has a cost. Using Yahoo's system, you can pay a 100 yen (about $1) fee to use a credit card, or 162 yen to do a bank transfer. There is a 0-yen method that I would like to learn how to use, which I think requires going to certain banks and paying at the ATMs there.
I'm able to pay using my bank's online system, too - the fee there is 100 yen unless it's to my same bank (those transfers are free). I compare that to eBay - the lowest shipping there seems to be $2, though it's usually $3 or $4 for just one card.
Speaking of shipping, I mentioned that dealers generally offer shipping at or under $1 for single cards. I recently received a 24-card set shipped for $1, and the three thick cards you see below were shipped for $1 total. I just won a 95-card set where the seller is charging $2 for basic shipping.
So, what have I been buying? Not that much, really, and it's mostly been cheap stuff. I bought my second and third series Calbee sets off Yahoo. In the past couple weeks I've been learning about how to make payments and using the communication system. Shipping addresses and such need to be typed in to each dealer, as well as telling the seller which bank the money was sent to (many sellers have multiple banks). With help from a coworker, I've essentially developed a form letter that I copy from auction to auction.
My first multi-auction win is a group of three cards from Immaculate Collection. I was bidding on another card that I didn't end up winning.
I can certainly see myself using Yahoo for MLB and NPB single cards as I get better and better at using the site. Much like eBay was wonderful for my collections in the late 1990s through mid 2000s, Yahoo opens up a whole world of merchandise in my (not-so-)new country.
By the way, eBay does still exist here, basically through the main portal site. But I imagine only savvy businesses selling Japanese goods to overseas buyers, and collectors of international things use it. (Keep in mind that shipping from the US to Japan is super-expensive.)