Counterbalance Meta-Library - "new views on complex issues from science, ethics, philosophy, and religion."
EpistemeLinks: Philosopy Resources on the Internet
Faith & Philosophy: Journal of the Society of Christian Philosophers
Guide to Philosophy on the Internet, from Earlham College
Internet Encyclopedia of Philosophy
The Ism Book - A Field Guide to the Nomenclature of Philosophy
Nicholas Berdyaev
Philosophy in Cyberspace
Philosophy Links from The Philosopher's Magazine. A massive collection of links arranged by historical period.
Philosophy Pages - includes a dictionary, history and a timeline.
Stanford Encyclopedia of Philosophy

Bible

Bible Dictionaries
Bible Gateway and another at Bible Versions and Translations
Bible History - a very brief summary
Bible Pronunciation
Bible Research: Internet Resources for Students of Scripture - a site " for Bible students who are looking for detailed information on the history of the canon, texts, and versions of Scripture."
Bible Study Tools at Crosswalk.com, including an Online Study Bible, Parallel Bible, Commentaries, Concordances, Dictionaries, Encyclopedias, Lexicons, History, Sermon Helps, Sermon Illustrations, and more.
Bible Views - "A Mennonite-Anabaptist Witness to Bible Teachings"
Blue Letter Bible - searchable King James Version with commentaries, dictionaries, maps, etc.
Brief History of the Bible
Daily Scripture Readings
Electronic New Testament Educational Resources by Prof. Felix Just, S.J. at Loyola Marymount University 
History of the English Bible
Into His Own - Perspective on the World of Jesus 
NetBible
New American Bible
New Testament Gateway
Online Bibles - a collection of links to Bibles around the web
Oremus Bible Browser provides a simple interface to the New Revised Standard Version of the Bible as well as the King James Version and several other versions of the psalms.
Resource Pages for Biblical Studies
Sacred Texts - Christianity
Society of Biblical Literature  - founded in 1880 to advance the public understanding of the Bible and biblical scholarship.
The Text This Week - variety of resources for study and liturgy based on the 3-year Revised Common Lectionary cycle
Transmission of the Bible to English
Unbound Bible - a collection of searchable Bibles consisting of: 10 English versions, Greek and Hebrew Versions, 4 ancient versions, and 42 versions in other languages. Also several tools, including a Bible dictionary, a commentary, Naves Topical Bible, Torrey's Textbook, Parallel View Search, and others.
Versions of the New Testament
World Wide Study Bible

Christianity

Biblical Christianity.info
Books and Culture
Call to Renewal
Catholic Encyclopedia
Catholic USA--links to almost 6,000 U.S. Catholic websites
Catholic Worker
Christ dot.org - "Christ. Period." - a blog
Christian Counterculture
Christian Ethics Today: Journal of Christian Ethics, published by the Christian Ethics Today Foundation.
Christian Faith and Postmodernity
Christian Link Collection--Anglican, Catholic, Lutheran, Orthodox, and Theological links, as well as other WWW Indices.
Christian Mystics
Christianity links from ARIL 
Church History Institute - interesting historical facts and biographical vignettes. And see their links page.
Commonweal--review of religion, politics and culture
Denominations Directory --a list of Christian denominations which is also searchable by location in the United States and Canda.
Eastern Orthodox Resources
Ecclesiatical Calendar
Ecclesiology: A Study in Church History
Ekklesia - a UK "think-tank that promotes radical theological ideas in public life"
Encyclicals and Other Papal Documents
Essays on Theology and Ethics by Kenneth Cauthen
Faith Central, from New Zealand 
Faithful America - "an online community of people of faith who want to build a more just and compassionate nation. It provides one-click opportunities to impact current political issues and shift the terms of public debate. It aspires to be an online wing of a powerful, new progressive faith movement, like the ones that fought for independence, abolition and civil rights.FaithfulAmerica.org is a project of the National Council of Churches with support from TrueMajority and Res Publica.
FaithResource
First Things
Godspy - "celebrates the passionate faith alive inside the Catholic Church"
Hauerwas on the Web
Jesus People USA
Jesus Radicals - see especially their essays on current events
Internet Christian Library--an extensive collection of resources including Christian literature and early Church documents.
Kingdom Now - "Founded to challenge the rampant nationalism in the churches of the United States after September 11, 2001, Kingdom Now serves today to connect and edify radical Christian communities." Here are found the 95 Theses On the Nationalistic Idolatry
of Churches in the United States. There are also excellent essays and other recommended reading in their library.
Moral Leadership: News and Notes from the Center of Christian Leadership
National Catholic Reporter
National Council of Churches
New Catholic Dictionary - "a project to put the 1910 version of the New Catholic Dictionary online. The Dictionary has thousands of short articles that clearly, simply explain aspects of Catholic life and influence. Many of the topics concern day to day things, practices and terms that have passed into obscurity, but deserve better."
Progressive Christians Uniting - "a movement of progessive Christians whose mission is to be a prophetic presence in the Church and in the world, steadfastly proclaiming the radically inclusive love of God and faithfully working for the inclusion of and justice for all God's children, regardless of sexual orientation, gender, age, race, ethnicity, or socio-economic status."
Progressive Theology.org - "a Christian alternative to the religious right"
Public Theology
Religion, Culture and Family Project
Religion Online
Religion Since 1945 from Fordham 
Religious History from Georgetown University 
SALT of the Earth
Seven Deadly Sins
Ship of Fools, "the magazine of Christian unrest" 
Sojourners--"to proclaim and practice the biblical call to integrate spiritual renewal and social justice." 
The Tablet--International Catholic Newspaper, with excellent links.
Theology Today -- ecumenical journal of theology published by Princeton Theological Seminary
Theological Resources on the Web, from America Magazine
Theology Library
U.S. Catholic--celebrates Catholic tradition, yet embraces the spirit of Vatican II reform and rejuvenation. 
National Conference of Catholic Bishops--Daily Readings, the NAB, the Catechism, Bookstore, Movie Reviews.... 
Using critical thinking regarding faith
The Vatican
Wittenburg Door
Zadok Institute for Christianity and Society

History

Ecclesiology: A Study in Church History
The Christian Catacombs of Rome

Significant Individuals

Dorothy Day
Bede Griffiths
Father Alexander Men
Cardinal John Henry Newman
Henry Nouwen
Padre Pio
Pope John Paul II
Francis Schaeffer
Alexander Schmemann

Publications

America
Catholic Dossier
Catholic Faith
Commonweal
Inside The Vatican
First Things
New Oxford Review

Miscellaneous Resources

Contemplative Outreach
Franciscan Cyberspot
Iconography -- dedicated to the art, spirituality, and theology of the Orthodox ligurgical art.
Ignatius Press -- Catholic Publishing House
The Orthodox Church in America
Stations of the Cross
Zenit News Agency -- News from Rome

Reference

The Busy Christian's Guide to Catholic Social Teaching, U.S. Catholic magazine.
Catechism of the Catholic Church
CatholicEducation.Org, -- excellent resource of articles by Catholic authors.
Catholic Encyclopedia [1917]
Christian Classics Ethereal Library - Classic Christian books in electronic format.
Guide to Early Church Documents
Guide to Online Sources in Medieval Spirituality
New American Bible Online, courtesy of the U.S. Conference of Catholic Bishops.
Theology Library

Web Directories

Catholic Information Center
Catholic Information Network
Catholic Resources on the Net
Christus Rex et Redemptor Mundi
New Advent
Resources for Catholic Educators
The Vatican

Faith and Science

American Scientific Affiliation, Science in Christian Perspective
Discovery Institute: Center for the Renewal of Science and Culture
God and Science - hypertext edition of Charles Henderson's study of religion and science, with chapters on Darwin, Marx, Freud, Tillich, Einstein, ...
Itest Faith and Science Page
Dialogue on Science, Ethics and Religion
Faith and Science, Catholic Perspectives
MetaNexus: The Online Forum on Religion and Science
Science and Faith Bibliography
Science and Faith Links--Christian and Muslim 

Islam

2 Discover Islam - from The Islamic Education and Services Institute
About Islam and Muslims, from Northumbria University
Introduction to Islam from The Middle East Institute
Islam 101, "an educational site on Islam, its way of life, civilization and culture."
Islamic Assembly of North America
Islam in America: From African Slaves to Malcolm X, from American Studies at UNC, Chapel Hill.
Islam Resources from ARIL 
Islamic Texts and Resources, from the University of Buffalo Muslim Student Association
The Koran, an online, searchable edition.
Map of the Muslim World, including Sunni/Shia distribution
Sacred Texts - Islam
Searchable Koran
View Islam, a Website intended "to provide English-speaking non-Muslims with basic information on Islam."
What is the Koran?, an excellent article from The Atlantic Online

Bawa Muhaiyaddeen Fellowship, devoted to Muhammad Raheem Bawa Muhaiyaddeen, a revered Sufi saint from the island of Sri Lanka.
Ibn Arabi Society, devoted to the Sufi saint & mystic.
Islam Online, Muslim web directory.
Islamic City, Muslim Web Directory
Ashki-Jerrahi, Local NYC Sufi Order.
Tafseer al-Mizan, An Exegesis of the Holy Qur'an

Judaism

Buber
Judaism 101
Judaism.com
Judaism Resources from ARIL
Reform Judaism
Sacred Texts -  Judaism
Talmud Torah
Tikkun Magazine
Torah.org - Center For Basic Jewish Education

People

Martin Buber
Rabbi-Maggid Yitzhak Buxbaum -- an excellent storyteller!
Reb Shlomo Carlebach
Rabbi Menachem Mendel Schneerson

Places

Virtual Jerusalem

Publications

Jerusalem Report
Tikkun

Reference & Resources

Chabad-Lubavitch in Cyberspace
FAQ on Hasidic Culture & Customs
Internet Judaica Starter Kit
Judaism and Jewish Resources
Judaism101
Project Genesis -- Online Torah Study
Soc.Culture.Jewish Newsgroups FAQ

Eastern Religions (Buddhism & Hinduism) 

Ammachi
Hindu Resources Online

Buddhanet
Buddhism Resources from ARIL 
Buddhist Peace Fellowship
Dharmanet
Resources for the Study of Buddhism - Compiled by Dr Ron Epstein, Philosophy Department, San Francisco State University 
Tricycle: the Buddhist Review

Interreligious Dialogue

The Los Angeles Buddhist-Catholic Dialogue, sponsored by the Buddhist Sangha Council of Southern California and the Catholic Office of Ecumenical and Interreligious Affairs.
Jewish Christian Relations.Net, owned and maintained by the International Council of Christians and Jews.
Jewish-Christian Relations: Recommended Links and Readings
Mission and Interreligious Dialogue, documentation, reports, and interconnections on interreligious dialogue in the ministries connected with the Jesuits in the United States.
Monastic Interreligious Dialogue, Established by the Benedictine Confederation in 1978 to assume a leadership role in the dialogue between Christianity and the great religions of the East.
Sedos.Org, [Servide of Documentation and Study], articles pertaining to interfaith & interreligious relations in the context of Christian mission.
The Society for Hindu Christian Studies, This is an organization for scholars and others interested in the study of Hinduism, Christianity, and the interrelations between these two religious traditions. 

Religious Studies

Web Directories

Academic Info: Religion
BeliefNet.Com
Facets of Religion
Internet Theology Resources
Mysticism in World Religions
Religion, Religions, Religious Studies
Religious Resources on the Net, searchable database of religious and Christian web sites on the Internet.
Virtual Religion Index, sponsored by Rutgers University. 

Reference

Religion Online - Full texts by recognized religious scholars.
Sacred Texts
World Scripture: A Comparative Anthology of Sacred Texts, edited by Dr. Andrew Wilson. International Religious Foundation, 1991. 

Other Sources Pertaining to a Range of Spiritual Traditions and Religious Expressions

BBC Guide to Religions of the World
Beliefnet
BELIEVE Religious Information Source - "a collection of over 2,000 articles by respected scholars on around 900 religious subjects."
Center on Religion and Democracy at the University of Virginia
DMOZ Religion and Spirituality
Digital Librarian--Religion and Philosophy
Divining America, Religion and the National Culture
Finding God in Cyberspace
Journalist's Online Glossary of Religion
Killing the Buddha--"a religion magazine for people made anxious by churches, people embarrassed to be caught in the "spirituality" section of a bookstore, people both hostile and drawn to talk of God."
Life of Rumi, founder of the Mawlawi Sufi order, a leading mystical brotherhood of Islam. 
Muslim-Christian Debate
Religions and Scriptures
Religious Movements Homepage at the University of Virginia 
Sacred Texts
Taoism, including English translations of the Tao te Ching
Tao Te Ching Translations: side by side comparison of 15 different versions
Virtual Religion Index, from Rutgers University 
Wisdom versus Knowledge, according to Hinduism
World Religion Resources from ARIL 
World Scripture

Mythology

Bullfinch's Mythology
Encyclopedia Mythica - "an encyclopedia of mythology, folklore, and legend"
Theoi Project - A comprehensive guide to the gods and other beings of ancient Greek mythology