I like to have physical books, so I mostly use Buyee, primarily on Amazon Japan. Buyee is a pretty standard proxy purchaser and shipping consolidator, but had some of the better prices that i found.
I also use Kinokuniya Australia when I can, but I find they often have things listed but unavailable.
I’ve been hunting some rare books, and in the past I used Buyee, but recently I tried to make some purchases and it threw some weird errors.
This time I’m trying FromJapan, we will see how it goes. Some of them come from Yahoo Auctions (BookOff Store), and some others that I couldn’t find there come from Rakuten/Rakuma.
I read manga on bookwalker, but for novels I’m not so fond of ebooks. Usually I would buy them from amazon.jp, but I always double check the title and isbn in ebay and abebooks. I’ve oocasionally picked up bargains on those sites, like three Keigo Higashino books for less than ten pounds!
It took me longer than I want to admit to figure out that while you cannot (or I cannot find a way) to download the ASCM file (to convert to EPUB) from the Japanese site, your Japanese and English site accounts are linked and you can download it from the English site.
I purchased 金田一耕助ファイル２ 本陣殺人事件 (natively link here) as my test book. I converted it to EPUB but on loading it into Yomu I did have to fiddle with it a bit to get it to read right to left and also it complained of not being a ‘properly formatted’ book lacking a table of contents or some such 
It’s functional but a bit sloppy - images are presented as half-cut off unless I select them to view in full.
I’m excited to try out Kobo as my main book site, though, as Bookmeter limits the number of highlights I can do which is a big drag. I want to highlight interesting things! Probably won’t get a full test immediately though as I have some other books to work through first 
So I just received my order of out-of-print books from FromJapan.
Can recommend them. If someone ever wants to give them a go, let me know, I can give a 500JPY discount.
I can also vouch for fromJapan. Used them for years and the worst issue is it takes a while for Suruga-ya orders to come in (though I think that’s due to Suruga-ya, not FJ.)
Those are some nice books, too!
Is it on purpose that you got one book twice? (G.U. volume 1)
just curious, sorry 
It was a test if anyone would notice!
Nah, actually it was a lack of plan purchasing it. My intention was to buy the volumes separately, but then I found out that vol 3 and 4 where not available for purchase. So I had to end up buying a Vol 1-4 set from a different seller.
I use amazonJP (they have the most affordable shipping cost for me - Europe) and Mandarake for used manga and light novels. 
With Mandarake I recommend purchasing from their Sahra shop because you can check the shipping costs afterwards. DHL is the most recommended if you’re from Europe. You will be required to send a copy of the order (screenshot is fine) as well as bank transaction copy to DHL during customs procedure and later pay applicable vat and/or customs but it’s super easy. In my experience they don’t charge much (I usually place around 10k jen orders and I get charged around 6% customs fee).
