Affiliates
• Desolate Dreams
Probably one of the first doujinshi collection sites that I visited in my early doujinshi collecting days and definitely one of the reasons why I started my own site. Jenn's taste in doujinshi is absolutely delicious. A perfect example of quality over quantity. If only I had the same restraint!
• Samurai-Blade
Rin and Jay's collection is full of things that I would easily covet -- their doujinshi by Pilgrim and Nagareya and Manna, for starters :D Between them both, they have collected from more fandoms than I have, and what they have is worth a look. And have I mentioned yet that the owners really are awesome? Cause they are.
Doujinshi Sellers
• eBay
Still a relatively good place to find doujinshi, but beware of the markup in prices. Shipping is sometimes unbelievable, but there are good, reputable sellers out there.
I just have to note that there have been issues in the past where doujinshi listings have been ended by eBay for violating copyright or some parent has complained about a seller selling their 10 year old kid "porn". So with this type of backlash to the sellers, many have stopped using eBay to sell. This is unfortunate but there are still other venues for sellers to use. It just takes a little searching to find them.
• Happy Otaku Site
Based in Japan and my personal favourite place to get doujinshi. Toshi, the owner, is an excellent seller who is unbelievable at finding stuff. He's found me doujinshi I didn't even know existed, and the price is just right. His collection is huge, spanning many anime fandoms, and he updates regularly. Also stocks regular, yaoi, and shounen-ai doujinshi, so the website's for everyone.
Toshi has also recently implemented a new shopping cart system as well as a new site layout, so it's even easier to get your hands on the doujinshi you've been looking for.
• JPQueen
Based in Japan, JPQueen offers used books and anime merchandise to the international community. Updated regularly and the prices are great as well. Also includes a legend that grades the condition of the doujinshi or item, which is very helpful. Also, if the doujinshi does not sell for a while, the price keeps getting lower and lower until it pracically hits rock bottom. Can't argue with that.
• Mandarake Online World Shop
You've heard of the store, now here's its website. Huge, huge, huge online shop filled with anything and everything related to anime and manga. A lot of it is sold out, but if you check back at the right time, you can definitely get a deal. Shipping is EMS only, which can get expensive, so I suggest buying more than one item to make it worthwhile. An upside to this is that your items are insured and they get to you faster. A warning to first time users, though: be prepared to stay a while and watch out for the hentai, if you don't want to see it.
• Shinjuku Station
At last—a doujinshi seller that lives in Canada! Shanna's site isn't fancy, but it gets the job done. And aside from selling doujinshi, she sells a lot of other things--shitajiki, binsen (doujinshi stationery), official ufo catchers, and other anime merchandise. And like most of the more personal shops, there is no shopping cart, but all it takes is quick email to her and Shanna gets back to you right away. I've found some stuff that I had been looking for from her and at reasonable prices. Highly recommended.
• Shopping Mall Japan
They don't sell doujinshi themselves, but they are the proxy bidding site that I use for bidding on Yahoo! Japan Auction. They're very good, and the turn around time for a question is about one day, though I've had some of my quesitons answered faster. The website is easy to navigate, and the doujinshi I've found on there, I probably would have never seen anywhere else. Good place to source the newest doujinshi as well.
• TokyoGetter
TokyoGetter is one of those hidden gems based right in the middle of it all. That, right away, is a major plus. You actually deal with the guy who goes out and looks himself. Talk about personal shopping! Turnaround time in response for a request is excellent as well despite the glaring time difference between Japan and Canada (where I am). I should also mention how personable Evan (the owner) is. You want to give him your business.
And doujinshi is not the only thing you can get. CDs, artbooks, toys... Basically, if it's Japanese, TokyoGetter can probably find it.
There's also a livejournal (tokyogetter) where there's stuff ready to buy.
• Twinbells Doujinshi
Another Canadian seller! Twinbells stocks a good amout of doujinshi in many anime, and the website is easy to navigate. No automated shopping cart system, but the response time is great, and since you communicate directly with the owner, you feel that you're really valued as a customer.
• Ultimate Anime
US based doujinshi website. Good shipping prices since they use flatrate envelopes if you buy more than one doujinshi, but the majority of their stock is of an adult nature. They also stock yaoi & shounen-ai doujinshi, for those inclined.