American Zen Teachers Assoc. list of Zen centers of members of the association.

Buddhism.org: According to their site, "This is the most comprehensive directory service providing all the resources of Buddhism and Buddhist from around world and trying to spread out Buddhism worldwide."

BuddhistDoor.com: I don't know much about this site but it's got some nice stuff.There's a link to their Buddhist magazine on their first page. Have a look at some very nice pictures of Buddhist art. Their archive is here. There is also a searchable glossary of Buddhist terms with some 700 terms. Translations of 20 sutras are also available here. Interesting site.

BuddhaNet file library: This is an excellent collection of Zen writings by a variety of authors, including  Robert Aitken, John Tarrant, Seung San, Master Sheng Yen, Katagiri, Maezumi, Ama Samy, as well as sutras, poetry and translations of some of Dogen's work. All in .zip files for fast downloading.

BuddhaNet's eBook Library: free ebooks for downloading. A good selection on Mahayana, meditation, art and general Buddhism.

BuddhaNet home page. Buddhist Studies: Interested in how a university teaches Buddhism? This link will take you to La Trobe University's Humanities & Social Sciences page on Buddhism. Twenty-five lectures on Buddhism are available here.

Buddhapia.com: This very large site includes Buddhist art, festivals & events around the world , Dharma talks by a wide variety of Buddhist teachers, temples around the world, sutra translations and much more. You can spend quite a long time here; an excellent resource.

Buddhist Peace Fellowship: well-established organization dedicated to social activism from a Buddhist perspective.
A collection of papers on various topics can be found here.

Dark Zen: This is an interesting, quite large site with many essays about Zen, some very critical of modern Zen practices.

Dogensangha.org: This is the home page of the group that follows Gudo Wafu Nishijima, translator of Dogen's Shobogenzo and Nishi Shobogenzo. 

Empty Universe: a nice collection of Buddhist writings broken into sections: Nikyay, Prajnaparamita, Vijnaptimatrata, Tathagatagharba, Sadhana, Bhavana, and Zen.

Glossary of Zen Names and Terms as Used in the Kwan Um School

Kalavinka Dharma Treasury: offers a collection of translations of Nagarjuna's writings for free or by donation as well as other writings. The site is run by Bhikshu Dharmamitra, a student of Ch'an Master Hsuan Hua.

Oryoki: The Practice of Soto Eating Bowls; Photos and instructions on traditional Zen eating ritual using oryoki bowls. Includes Dogen's Instructions for the Tenzo and meal chants.

Sotozen.net: Home page of the Soto sect. Includes list of Soto temples & centres worldwide and a list of temples where foreigners can stay in Japan.

Taitong Temple: this is the temple of Dogen's teacher, Rujing, and where Dogen settled the Great Matter. Therefore, an important temple in Japanese Zen history. The site is quite wonderful with photos, writings, history, etc. However, be warned, it is yet incomplete so it's a site worth keeping an eye on although now (Feb, 2007) it's still worth visiting.

Tibetan Buddhism: The Government of Tibet in Exile has some excellent resources here on various aspects of Tibetan Buddhism.

Stephen Batchelor home page: Batchelor is the author of Buddhism Without Beliefs (review here) as well as numerous other books and articles. His home page includes access to a number of his articles.
The Agnostic Buddhist: "Edited version of a talk given at the symposium "American Buddhism Today" to celebrate the 30th anniversary of the Rochester Zen Center, Rochester, New York, June 22, 1996."
Shaping The Future? Western Buddhist Teachers Meet the Dalai Lama: Dharamsala, India. March 23-22, 1993

Engaged Zen Foundation: this organisation teaches Zen to prisoners in the U.S. There is a very interesting comic book published on this site about learning zazen. This is tough Zen.
A poignant essay by Rev. Kobutsu Malone about his battle to save a death row inmate can be found here.

The Gospel of Buddha by Paul Carus Originally published in 1894, this is one of the earlier books introducing Buddhism to the West. The entire book is now available online.

Women in Buddhism The Buddha's teachings for women, as well as many articles and books by or about women in buddhist history, past and present.

Philip Yampolsky: was one of the great Zen translators. This is a brief biography/obituary of this Buddhist scholar.

Zen Centres of the World: A comprehensive list of world-wide Zen centres. The Australian list is here. Soto Zen Centers around the world; includes names, addresses and phone/fax/email.

Zen Stories to Tell Your Neighbours: an interesting little collection of Zen stories, many based on koans. Sort of a mini Zen Flesh, Zen Bones; by John Suler, academic psychologist at Rider University. Somewhat entertaining.