MusicaSacra - The website of the Church Music Association of America. Includes several resources such as e-publications, forums, audio, and CMAA membership information. Also of particular interest are the archives of Caecilia, Sacred Music, and Gregorian Review.
Cantus - indices of the Latin ecclesiastical chants found in early manuscript and printed sources for the liturgical Office, such as antiphoners and breviaries.
Analecta hymnica medii aevi - Contains authoritative texts of hundreds of medieval hymns.
Hymnary - a comprehensive index of hymns and hymnals.
Choral Public Domain Library - Over 2800 scores available for free in PDF format. Lists other free sites.
Cyber Hymnal - Lyrics, scores, MIDI files, pictures, history, and other information on over 2,300 Christian hymns and gospel songs from many denominations.