Collections of Links:

Handbook of Latin American Studies from Library of Congress:
https://guides.loc.gov/handbook-of-latin-american-studies

DIAMM (the Digital Image Archive of Medieval Music)
https://www.diamm.ac.uk/

Portuguese Early Music Database
http://pemdatabase.eu/

Best of the Web The New York Public Library (no longer updated but useful nevertheless)
https://www.nypl.org/weblinks/2473

Digital Resources for Musicology
DRM (ccarh.org)

National Library Sites:
Europeana, a portal for searching holdings of many European national libraries and other important research libraries (replaces older theeuropeanlibrary.org):
https://www.europeana.eu/en

significant individual sites:
Bibliothèque nationale de France
bnf.fr

Biblioteca Nacional de España
http://www.bne.es/es/Inicio/index.html

Deutsche Nationalbibliothek (DNB)
https://www.dnb.de/DE/Home/home_node.html

Österreichischen Nationalbibliothek
https://www.onb.ac.at/

Composer sites:
Portuguese composer Oscar Lorenzo Fernândez (1897-1948):

https://lorenzofernandez.org/

Brazilian composer José Maurício Nunes Garcia (1767-1830)
josemauricio.com.br

Medieval Music:

La Trobe University Library Medieval Music Database
Modern scores and facsimiles of original manuscripts; although no longer maintained, still provides considerable important content

Thesaurus Musicarum Latinarum
"...free access to and make searchable every known Latin text on music from the late antiquity to the seventeenth century, in multiple editions and in transcriptions from original sources."

Abbaye de Solesmes
From the abbey renowned for spearheading the revival of Gregorian chant in modern times

The British Library Catalogue of Illuminated Manuscripts
full text facsimiles of Medieval and Renaissance manuscripts
 

Renaissance Music:

RELICS Renaissance Liturgical Imprints: A Census

Hill Museum & Manuscript Library
a vast database of manuscript images, including music, from St. John's University and St. John's Abbey in Collegeville, MN; includes the Renaissance and much more

Classic and Romantic Music:

The Ira F. Brilliant Center for Beethoven Studies  from San Jose State University
 

Ethnomusicology:

Ethnomusicology
Ethnomusicology, Folk Music, and World Music  an important ethnomusicology portal from the University of Washington

British Forum for Ethnomusicology
"a UK society devoted to the study of music and dance from all parts of the world"

Ethnomusicology
the journal; a website providing information about it with sample full-text articles

Other:

Center for the History of Music Theory and Literature
from Indiana University; includes Doctoral Dissertations in Musicology and several research sites
Includes Thesaurus Musicarum Latinarum