I read a lot of books, and recently I have switched over to ebooks because for some reason I find them easier on my eyes. There are a few factors that complicate access to Japanese ebooks - whether or not you have a Japanese credit card or a Japanese address and whether or not there is an app available for your country.
Really, I would love to use Amazon Japan Kindle - especially if there were audible versions tied in so that I could read and listen at the same time. That is my ideal, but my old work around of using gift cards doesn't seem to work anymore and I have neither a Japanese address nor a Japanese credit card. If I did though... I totally would. Instead I have looked for alternatives.
Each website offers different options, and often uses its own proprietary reader, even if the titles are the same. So, it makes sense to do some exploring before deciding which one(s) you prefer as a go-to source. n my case, I sample here and there, but because I am limited to using a US credit card, there are only a few options for me to actually buy digital copies of the manga that I want to read.
I have been using eBookJapan the longest. It has made some changes recently by merging with Yahoo! Japan so that Japanese folks can use Yahoo! Japan money, but I am still able to use a US credit card it is just a little more complicated (and I went in many circles before I got signed up correctly). But more importantly to me, eBookJapan dropped support of its overseas app, and that means that I am limited to storing my books online and reading on the browser instead of a reader on my iPad. I just tried to help a friend make the move over to the new eBookJapan and there is a new twist that requires a Japanese cell phone number, which is a big problem for us.
That doesn't make me happy so I decided to explore other options.
BookWalker is another site that I have looked at this year. It includes manga, light novels, novels, nonfiction, game strategy books, and interestingly enough doujinshi. There is a sister site called BookWalker Global for the English translations of manga and light novels. So, flipping between the two can really be useful if you are the type who wants to read first in English before dipping into the Japanese (or vice versa). There are lots of manga that are available for free for a limited amount of time.
Now the BookWalker Global website does allow payment by PayPal. There are also notes about licensing restrictions (the English language editions not allowed to be sold in Japan) And if you are wanting to look for the Japanese original of a manga/light novel that you enjoyed, look at the product details towards the bottom of the page.
Kinoppy is the ebook service/reader used by Kinokuniya. It is possible to sign up from overseas and to pay using a Japanese credit card. Not all the e-books are licensed for overseas use though, so be aware. I will say that the ones I saw that I wanted but couldn't buy in Kinoppy were available in BookWalker:) So keep both sites open as you search.
Honto.jp is a website I use all the time for tracking down titles, looking at samples (and tables of contents for anthologies). It sells both print books and ebooks. It accepts foreign addresses and foreign credit cards. Its app isn't available overseas for iOS, but I can download the app for my laptop or read online. So for me, it loses some of its appeal for curling up and reading, but it is a wonderful collection.
CMOA is an example of a comics/light novel website that offers a monthly subscription to either unlimited or limited (missing BL, TL, light novels aka the good stuff) but only accepts credit cards issued in Japan. So, that lets it out for me. BUT, there is a free login option that you can use to either read through the browser or use the reader. The reader (bookshelf) application is available for Windows, iPad, and Android.
If you want to use the website for research – looking at rankings, genres, etc. The categorization is pretty good and I really appreciate the adaptation (which titles have been picked up for anime, movies, dramas) information.