• African Association for the Study of Religions (AASR)
• American Academy of Religion (AAR)
• American Anthropological Association (Section on Religion)
• American Sociological Association (Section on Religion)
• Associação Brasileira de História das Religiões (ABHR)
• Asociación de Cientistas Sociales de la Religión en el Mercosur / Associação dos Cientistas Sociais da Religião do Mercosul (ACSRM)
• Association for the Study of Esotericism
• British Association for the Study of Religions (BASR)
• British Sociological Association (Religion Study Group)
• Canadian Corporation for Studies in Religion (CCSR)
• Canadian Society for the Study of Religion - La Societé canadienne pour l'étude de la religion (CSSR/SCÉR)
• Center for Studies on New Religions (CESNUR)
• Centre d’Etudes Interdisciplinaires des Faits Religieux
• Council of Societies for the Study of Religion (CSSR)
• Council on Graduate Studies in Religion [U.S.A.]
• Dansk Selskab for Religionshistorie - Danish Association for the History of Religions (DAHR)
• Deutsche Gesellschaft für Geographie (Arbeitskreis Religionsgeographie)
• Deutsche Gesellschaft für Soziologie (Sektion Religionssoziologie)
• Deutsche Vereinigung für Religionsgeschichte (DVRG)
• Ecole Pratique des Hautes Etudes (Section des sciences religieuses, Sorbonne, Paris)
• European Association for the Academic Study of Religions / Association Europeenne pour L'etude Scientifique des Religions (EurAssoc)
• European Association for the Study of Religions (EASR)
• Hartford Institute for Religion Research
• International Association for the History of Religions (IAHR)
• International Society for the Sociology of Religion (ISSR/SISR)
• Japanese Association for Religious Studies (JASRS) [site in Japanese]
• Japanese Association for the Study of Religion and Society (JASRS)
• Korean Association for the History of Religion (KAHR)
• Nanzan Institute for Religion and Culture [Nagoya, Japan]
• Nederlands Genootschap voor Godsdienstwetenschap / Netherlands Association for the Science of Religions (NGG)
• North American Association for the Study of Religion (NAASR)
• Religious Research Association [U.S. think tank]
• Romanian Association for the History of Religions (RAHR)
• Schweizerische Gesellschaft für Religionswissenschaft (SGR)
• Sociedad Española de Ciencias de las Religiones / Spanish Association for the Science of Religions (SECR)
  
• Società Italiana di Storia delle Religioni
• Société Québécoise pour l'étude de la religion (SQER)
• Société, Droit et Religion en Europe
• Society for the Scientific Study of Religion (SSSR)
• Society for the Anthropology of Consciousness (SAC) [section of the American Anthropological Association (AAA)]
• Society for the Anthropology of Religion (SAR)
• Ústav pre vztahy štátu a cirkví (Institute for State-Church Relations) [Bratislava]

There are many other organizations for the academic study of religion which apparently do not have websites (see the list of IAHR member associations).

Journals

Portals

• Center for Electronic Resources in Theology and Religion Electronic Journals Gallery
• The Register of Asian & Pacific Studies Electronic Journals
  

Online/Full-text Journals

• Electronic Journal of Vedic Studies
• Esoterica
• Japanese Journal of Religious Studies
• The Journal for Cultural and Religious Theory
• Journal of Buddhist Ethics
• The Journal of Religion and Film
• The Journal of Religion and Popular Culture
• The Journal of Southern Religion
• Revista de Estudos da Religião (REVER - Portguese, French, English)

Limited Access Journals (abstracts, sample issues)

• Anthropos
• CrossCurrents
• History and Theory
• History of Religions
• International Journal of Hindu Studies
• Journal of the American Academy of Religion
• Journal of Cognition and Culture
• Journal of Contemporary Religion
• The Journal of Religion
• Journal of Religion and Society
• Method and Theory in the Study of Religion
• Religion
• Religion Staat Gesellschaft. Zeitschrift für Glaubensformen und Weltanschauungen
• Studies in Religion / Sciences Religieuses
• Zeitschrift für Religionswissenschaft

Research Tools

• Hartford Institute for Religion Research's list of sociologists of religion

SuperSites

• Virtual Religion Index
• Academic Info: Religion Gateway
• Facets of Religion (on-line texts and resources organized by tradition - mirrored from wwwvirtualibrary)
• Finding God in Cyberspace (John L Gresham's Guide to Religious Studies Resources on The Internet)

Theory and Method

• REVER Special Issue on "Theoretical Issues in the Study of Religion" (articles by Gregory D. Alles, Michel Despland, Francisco Diez de Velasco, Steven Engler, Daniel Gold, Gregory Price Grieve, Wouter J. Hanegraaff, Marsha Hewitt, Titus Hjelm, Kim Knott, Jens Kreinath, Luther H. Martin, Claudia Schippert, Robert A. Segal, Paul L. Swanson/James W. Heisig, and Ann Taves)
• Bibliography of Cognitive Science and Religion
• The Method and Theory Bibliography Project (bibliographic references searchable and indexed by sub-field)
• Theory and Method Web Resources (Gene R. Thursby)
• Weberian Sociology of Religion (Moriyuki Abukuma): full-text editions, thematic overviews, and critical resources
• Robert Alun Jones -- Critical synopsis of Durkheim's The Elementary Forms of the Religious Life (1912)
• Experimental Studies of Supernatural and Religious Concepts (página de links a artigos, juntados por Pascal Boyer, uma das figuras mais importante no campo - muitos links quebrados)
• International Association for the Cognitive Science of Religion (a primeira e única associação profisional dedicada a esta teoria)
• Institute of Cognition and Culture (importantíssimo local, em Belfast, da institucionalização desta teoria)
• Cognitive Science of Religion Series (a primeira série de livros dedicada a esta teoria)

This is a selective, incomplete, and often slightly out-of-date list of resources. Link suggestions?