Three major ones, followed by a short alphabetical list of smaller ones. WESSWEB Medieval and Renaissance Studies has a more extensive list, with links.
The primary work of the International Medieval Institute, found in 1994 and located at Leeds University in England, is production of the International Medieval Bibliography, and organizing, hosting, and publishing the proceedings of the International Medieval Congress. This conference is the largest annual gathering of European medievalists.
Founded in 1925, its goal is to support research, publication, and teaching in medieval art, archaeology, history, law, literature, music, philosophy, religion, science, social and economic institutions, and all other aspects of the Middle Ages. This organization publishes Speculum, which is a major journal in this field, grants money to assist scholars in publishing in the field, has an annual conference.
Founded in 1961 at Western Michigan University, it is a center for teaching and research in the history and culture of the Middle Ages. Offered the first M.A. in medieval studies at a state-supported university in the U.S. Hosts the annual International Congress of Medieval Studies in May each year. Richard Rawlinson Center for Anglo-Saxon Studies and Manuscript Research is here, which is producing the online SASLC, Sources of Anglo-Saxon Literary Culture. Hosts the EDAM, Early Drama, Art, and Music Project, coordinating and sponsoring research in early drama and encouraging interdisciplinary study relevant to the theater. The Medieval Institute also publishes many secondary works, new editions of primary works, and also The Medieval Review, a major journal in the field.
Links to primary and secondary sources, plus a bibliography.
Besides information about the organization there are links to other medieval sites.