So you want to read manga in Japanese, but you don't live in Japan. How do you get some? This question has consumed me for the past
Due to how the Japanese book market works, new books are only available at cover price and rarely discounted (as far as I know). Only the most popular books get multiple printings and stay on the market for many years; more obscure books may sell out in the space of months or years and never see additional printings. Thus availability of a book is best shortly after its release. Naturally, tracking down used books is hard when you live outside Japan, with some exceptions.
Buying New (Brick & Mortar)
By far the easiest way to buy manga is to walk into a store and get it right off the shelf. It is not the most economical route, as you will pay roughly a third over the cover price, but it is actually fairly competitive with the cheapest methods of shipping from Japan. In the United States, I've only been to Kinokuniya and Sanseido; there's also Asahiya. They are basically Japanese bookstores; the staff understand English but often they may not be very confident in it. Both Kinokuniya and Sanseido will take special orders for things they don't happen to have on the shelf; it takes about a month and they let you know when it comes in via postcard or phone.
Kinokuniya is a Japanese bookstore chain with locations around the world. In the U.S., they have locations basically on the West Coast (San Francisco, Seattle, Portland, San Jose, Los Angeles, Costa Mesa) and in NYC. I've been to the ones in SF, SJ, and NYC, and the experience is fairly consistent. The SF store, located on two floors of the west block of the Japantown mall structure, has its lower floor devoted to manga and otaku goods. While my memories of the NYC store are hazier, they have substantial floorspace dedicated to manga. The San Jose store is only one floor and has less manga. You can use Kinokuniya's online system to look at their inventory, broken down by store.
Kinokuniya shrinkwraps its manga and magazines, though light novels and other books are not shrinkwrapped. Pricing has a built-in markup that covers their costs; there's a price tag on every book which is often very annoying to remove. Magazines do not have this price tag; instead a table of exchange rates is posted. Kinokuniya doesn't have a point card system, but they have a "manga club" where you pay an annual fee and get lower prices on manga.
It looks most, if not all, of the Sanseido stores are now Kinokuniya branches.
Asahiya is a Japanese bookstore chain whose U.S. locations are limited to Southern California. They used to have locations in NYC and Chicago. I don't know much beyond that.
Buying New (online)
If you don't live near one of the above-mentioned brick and mortar stores, your best option is buying online. At first blush, buying online looks inexpensive: "Wow, 600 yen per volume!" However when you take shipping into account, as well as the potentially long wait, the picture is less rosy. That said, buying online direct from Japan is the surest way to get exactly what you want, and often at a reasonable price (though the exchange rate has been in the doldrums).
bk1 was my preferred online bookstore due to their promotions, point system, and range of shipping options (EMS to Sea Freight). As of May 2012 they've merged with the e-book site honto. Before the merger there were rumors that the new entity would stop accepting new international customers, but so far it it doesn't seem to be true. Japanese users (on 2ch) are apparently mad about not having coupons anymore, but time will tell how it all shakes out.
The main drawback is that the website is available only in Japanese. You can use Rikaichan to remedy that, though. The selection and search is pretty good. They display the lead-time for each item next to the description; however, I've ordered some "7-21 day" items, only to get an apologetic email saying they weren't able to track any down. That only happens if you order obscure/old things though. Another minor drawback is that the exact shipping costs are not known until your order ships, but you can make an estimate with their rate tables. (You can also look at my order stats. I usually get Sea Freight since I'm cheap.)
So far honto has kept the 1000 points on 10000 yen promotion, and they occasionally run 300/500 points on 3000 yen promotions. However it seems that promotional points expire quickly (in about a month), which makes it less worthwhile if you only buy a few times a year. All things considered, it's still probably one of the cheaper ways to get books from Japan.
I'm not sure when it changed, but I guess it doesn't work the same way anymore. It looks like Japanese books are shipped directly to you from Japan.
Although CDJapan deals mostly in CDs, they have a selection of books and manga. So far I've only taken advantage of their magazine subscription system, which is pretty cool. Their manga range is wider than I expected, so I might try them out when there's a CD I want to buy. They offer SAL, have a shipping calculator, and have a point system.
YesAsia carries manga, along with a whole bunch of other Asian media. They build a markup into the item price and offer free shipping on orders over ~$40. I haven't done the math, but it seems to be an okay deal. Their manga selection isn't as wide as other sites, but they have most popular things. What's soured me on YesAsia is that I've received some books with telltale signs of cover wear. I'm picky about the condition of my books, so I don't order manga from them anymore.
I used to not recommend amazon.co.jp, since they have limited and expensive shipping options, with a linear dependence on item count. However I've become aware that manga sets count as single items... so that's one weird trick you might be able to take advantage of. If you buy individual volumes, though, it's not so great. They have a large selection and a familiar English interface option, so if you have money to burn, it's an option. (Amazon also has lots of tantalizing ¥1 used manga, but those guys generally only ship domestically.)
Buying used is the absolute cheapest way to get manga, and a great way to broaden your horizons — if you're lucky enough to have a Book Off in your neighborhood.
Book Off is a chain of used bookstores with locations in Japan, the U.S., Canada, France, and Korea. In the U.S. there are stores in Hawaii, the LA area, San Diego, and NYC. For a manga fanatic, it's almost too much to bear: shelves upon shelves of $1 manga. Random sales that make the price 80 cents, or 2-for-1. While the condition of the $1 manga is sometimes sketchy, more often than not they're just a bit worn, and sometimes in pretty darn good shape. Besides the $1 section, there's also the ~$5 section, where books are sometimes, but not always, in better shape. You rarely find a complete set in the $1 section, but the fun is in repeated trips.
Acclimate Solution, located in Japan, offers a selection of new and used manga. They have an ebay store and also take requests; you tell them what you're looking for, and they send you a quote. I've gotten a few hard-to-find books through them.
Japan Book Club: A Japanese-business-for-Japanese-people sort of place that I learned about by reading Adam Stephanides's blog. There's a rather small selection of used manga at the Chicago location, and it appears to go for $3 and up.
eBay: If you lurk, you can score good deals on manga. I got MangaScreener's founder's collection of Happy! this way.
jpqueen: Have not used this site, but other people do.
Tenso: Forwarding service. I use this if I have no other choice.