Research Tools
COPAC: Access to the unified online catalogues of some of the largest university research libraries in the United Kingdom and Ireland.
ITER: A gateway to studies in the Middle Ages and the Renaissance that includes an online bibliography covering all languages and disciplines from 400 to 1700.
The Labyrinth: Resources for medieval studies.
Luminarium: Provides texts and supplemental materials for medieval and Renaissance studies.
Medieval and Renaissance Studies: Lists library collections online, primary text archives, medieval studies projects on the Internet, manuscript projects, and digital exhibitions.
NetSERF: A comprehensive index of medieval resources on the Internet.
The ORB: An online reference book for medieval studies, written and maintained by medieval scholars.

Programs and Organizations (Most of these sites have extensive links collections for further research.)
ACMRS: Arizona Center for Medieval and Renaissance Studies.
AVISTA: Association Villard de Honnecourt for Interdisciplinary Study of Medieval Technology, Science and Art, which includes an online publication of AVISTA's journal.
Center for Medieval Studies: At Fordham University.
Center for Medieval Studies: At the University of Minnesota.
Centro Elaborazione Informatica di Testi e Immagini nella Tradizione Letteraria: At the Scuola Normale Superiore in Pisa.
Feminae: The Medieval Women and Gender Index showcases scholarship on women, gender, and sexuality during the Middle Ages.
Institute for Medieval Studies: At the University of Leeds.
International Center of Medieval Art: Extensive listings of events and resources.
Italnet: Guide to online projects in Italian studies, including the Opera del Vocabolario Italiano, a full-text database of more than 1,300 early vernacular texts.
The International Courtly Literature Society: With regional branches worldwide.
Medieval Academy of America: Offers Medieval Academy News online and sponsors fellowships, grants, and prizes.
The Medieval Institute: At Western Michigan University.
Medieval Research Centre: At the University of Leicester, which includes information about its MA program and other research opportunities.
Medieval Studies Certificate Program: At the Graduate Center, City University of New York.
Medieval Studies Program: At Rutgers University.
Medieval Studies Workshop: At the University of Chicago.
The Metropolitan Museum of Art: In New York City.
The Morgan Library & Museum: In New York City.
The New York Public Library: Access to online catalogues of texts.
Renaissance Studies Certificate Program: At the Graduate Center, City University of New York.

Manuscript and Text Studies
The Aberdeen Bestiary: The digitized version of the manuscript with an English translation and transcription of the original Latin and commentary.
British Library's Digital Library: Digital editions of rare historic texts.
Centre d'Etudes des Textes Medievaux: de l'Universite de Rennes. An online collection of French medieval texts.
The Chronicles of Froissart: Electronic version of the John Bourchier translation.
Digital Scriptorium: A searchable image database of medieval and Renaissance manuscripts from many institutions.
Early Manuscripts: At Oxford University. An extensive collection of digital facsimiles of early manuscripts.
The Electronic Beowulf Project: A huge database of digital images of the Beowulf manuscript, as well as related manuscripts and printed texts.
Electronic Text Center: University of Virginia's online archive includes over 45,000 classic texts in 12 languages, including a Middle English collection, an Old English corpus, and a variety of Renaissance sources.
Gallica "Classique": Provides full texts of major works of French writers of the Middle Ages.
Greek and Byzantine Paleography Web Links: Maintained by Paul Halsall.
Internet Medieval Sourcebook: Texts of medieval sources.
Middle English Compendium: Database of Middle English works and manuscripts.
Moralia in Job: An online English translation.
Roman de la Rose: Online manuscripts of the Roman de la Rose.

Manuscript Catalogues
Catalogue of Medieval Manuscripts: Trinity College, University of Cambridge.
Corsair: The Pierpont Morgan Library.
The Department of Special Collections and Western Manuscripts: Bodleian Library, University of Oxford.
Manuscripts Catalogues: The British Library.
Medieval Manuscripts: St. John's College, University of Cambridge.

Art and Archaeology (For manuscripts, see above: "Manuscript and Text Studies" and "Manuscript Catalogues.")
Amiens Cathedral Project: Columbia University.
The Bayeux Tapestry: The complete tapestry in digital form.
The Corpus of Romanesque Sculpture in Britain and Ireland: A searchable digital archive.
Index of Christian Art: Princeton University.
Medieval Art in Pisa: Includes links, images, and historical data.
Wall Paintings in Danish Churches: An image database.

History
The Geography of Roman Gaul: University of South Carolina.
Institute of Historical Research: The IHR's digital library containing some of the core printed primary and secondary sources for the medieval and modern history of the British Isles.
Manuscripta Mediaevalia: A database of German medieval manuscripts and handwriting samples.
The Medieval Science Page: A comprehensive set of links.
Mittelalterliche Frauenkloester: Links and information for scholars working on medieval women's studies.
Quellen zur mittelalterlichen Reichsgeschichte: Medieval German history.
Society for Late Antiquity: University of South Carolina.
Virtuelle Bibliothek-Geschichte: Medieval history.

Religion
Bibleserver.com: A site with a variety of translations of the Bible into many languages, including Vulgate, Hebrew, LXX, and Arabic with a feature that shows all the versions for one verse.
Bibliographies: Bibliographies of medieval and Franciscan preaching, medieval exegesis, Franciscan historiography, and Franciscan travel and missionary works.
Bibliography: Medieval Spirituality: Links to bibliographies on medieval mysticism, Benedictine and Cistercian monasticism, the Franciscans, the Dominican mystics, and other medieval mystics.
The Catholic Encyclopedia: Extensive online encyclopedia of Catholic history, practices, and beliefs.
Christian Hagiography: Societe des Bollandistes.
JewishEncyclopedia.com: The online version of the 12-volume Jewish Encyclopedia, originally published between 1901 and 1906.
Medieval Monasticism: Links to resources on monasticism in the Middle Ages.
Monastic Matrix: A collection of resources for the study of women's religious communities from 400 to 1600.

Medieval & Renaissance Drama
Castle of Perserverance  text of the English morality play, interpreted in modernized language as a teaching aid
Medieval European Drama in Translation: An online bibliography of published English translations of early European drama.

Anglo-Saxon Studies
Tha Engliscan Gesithas, the society for people interested in Anglo-Saxon language and culture
Sermo Lupi ad Anglos
Matheliende, the Newsletter of Anglo-Saxon Studies at the University of Georgia

Patristic Studies, Late Antiquity
Bibliographic Information Base in Patristics:  searchable in French, with introduction available in English
Canadian Society of Patristic Studies
Patrologia Latina
The Ethereal Library, Study Bibles and Early Church Fathers in electronic format

Celtic Studies and Irish Studies
CELT, Corpus of Electronic Texts
Celtic Studies Association of North America (CSANA) homepage

Publishers
Association of American University Presses, online catalog
Brepols Publishers
Moleiro, publishers of replicas and art books
University of Chicago Press
University of Illinois Press
University of Michigan Press
University of Toronto Press
Cornell University Press
Indiana University Press
Oxford University Press
Yale University Press
Cambridge University Press
Routledge Publishers
Homepage for Dante Studies
: Italian Studies.
Johns Hopkins Press

And...
Misconceptions about the Middle Ages, an electronic book generated by the Medieval Religion discussion list
Bede.net, an academic resource for the study of the Venerable Bede
Museum Replicas Limited, when you need "historically accurate, battle-ready" swords, axes, helmet, shields and chain mail