Japanese Sword Society of the United States - A good organization that has a good newsletter. They are also hosting the Nihonto Knowledge Base, an application I wrote to help with online smith research. This is the national organization that I recommend new collectors to join in preference to the other choices available.
Nihontoclub - most extremely excellent online resource for researching swordsmiths. Community run.
NBTHK Tokyo Japan - the Nippon Bijutsu Token Hozon Kyokai is the primary organization for assessing and attributing Japanese swords. They issue papers, and maintain a museum (well worth a visit).
Nihonto Message Board - Brian Robinson's discussion board, a great place for new people to come online and ask questions and get the benefit of community wisdom... all without having someone stick a thumb in your eye for having asked a newbie type question. Ebay talk is not allowed.
Nihonto Kanji Pages - Rich Turner's most excellent reference on kanji used for swords and tosogu. A great resource for anyone who wants to learn to read inscriptions, it is organized to economize your efforts at learning the most important kanji.
Kendo Katori - an extremely good dojo in Moscow, Russia, with high level teachers in tameshigiri, kendo, aikido and other Japanese martial arts. I've sampled the instruction myself, it's serious and no-nonsense but done so in a bright and friendly atmosphere. It is most highly recommended to make contact with this club if you are visiting Moscow or resident there.
Nihonto Knowledge Base - The Nihonto Knowledge Base is a web application I wrote for people to research smiths. I donated the use of code to the JSSUS and they are currently running it on their website under "Research." Only guaranteed to work under IE and Mozilla Firefox as it uses all kinds of funky tricks, but should work mostly right I think on anything.
You do in this world have to be careful with whom you deal. I have been unpleasantly surprised in the past by how some people have treated me when I was their customer and they thought the money had dried up as positive statements to your face can turn into negative statements behind your back or said to your contacts. Money is the primary motivation of a lot of people and there is not a lot of honor in their behavior because of this. This is one thing about the competitive nature of any business is that because money is at stake, competitors do not often have good things to say about each other and some are not above telling lies or making exaggerations in order to spread fear, uncertainty and doubt.
The below people are those that I have enjoyed doing business with and I like and trust as people. Everyone in the world will have different experiences, and it's important for any customer to use their own judgment and not trust anyone blindly. So use your best discretion when shopping for a sword and be sure to take care of your own interests.
Markus Sesko an author and translator, I recommend all his books and if you need sword information translated, he is the man to talk to.
Swords of Japan - run by Ray Singer, a reliable and knowledgable source for swords
Grey Doffin is a long time collector who also has some good videos around about sword care. He's also contributed to some of the good free research materials at the JSSUS with his Index of Japanese Sword Literature.
Alf Tan - Serving the under-serviced segment of the sword market, Alf Tan's site has lower priced items and bargains a plenty.
Bugei - If you're interested in a modern made blade for cutting practice, Bugei has a good selection of swords made inspired by Japanese techniques which are robust, and appropriate for sporting use and very effective cutters.
Legacy Swords - Ted Tenold is a sword polisher and maintains his services as well as some antique swords for sale on his own website.
Moses Beccera - Moses Becerra is a sword polisher and dealer in New York. He has shown me swords he's polished, and they have been treated excellently.
Japan Sword - A Japanese site run by the Inami family. Friendly and good people, I often recommend people to go to them if in town, or in need of services inside Japan. They have treated those I've sent very well.
Iida Koendo - A Japanese site run by the Iida family, dealers since the Meiji period. High end items!
Ginza Seikodo - A Japanese site run by Hisashi Saito san, also dealers since the Meiji period. Highly recommended.
Shobudo - In Japan, run by Masahiro Ohira, he speaks good English and is very helpful and reliable.
Satcho - Michael has a very broad selection of Nihonto related books, ships quickly and is a joy to work with.
Tsunahiro - Swordsmith in Kamakura Japan. It's possible to visit his shop and buy a sword or supplies. I once brought back a lot of his hocho for my website and they are quite nice.