Below are selected resources for organological research. Expand the sections for links. 
Due to the large number of public collections, and the ease of locating them through general internet searches, they are not included here.

This page is under development and may change soon. Please make suggestions including additions and corrections here.

  Clinkscale Online: The Database of Early Pianos up to 1860 (MIRCAT)

  Boalch-Mould Online: Makers of the Harpsichord and Clavichords and their Surviving Instruments (MIRCAT)

  Musical Instrument Museums Online (MIMO)

  MINIM-UK (Musical Instruments Interface for Museums and Collections)

  Historic Trombone Database

  Extant Lutes Database

  Viols Database - Viola da Gamba Society of America

  The British Institute of Organ Studies - National Pipe Organ Register

  Reed Organ Society Database

  Renaissance Recorder Database

  Smithsonian Online Virtual Archives (SOVA)

William Dowd records (link)
Frank Hubbard records (link)
John Challis records (link)
Chickering & Sons Piano Company records (link)
Hugo Worch photos (link)

  Online Archive of California (OAC) 

Bjarne Dahl Restoration Reports (link)
Strong Museum Collection: Aeolian Company; Mason & Hamlin, piano makers  (link)
Peter Adams collection of musical instrument catalogs (link)
Richard J. Howe collection of musical instrument literature 1838-2002 (link)
Catgut Acoustical Society Newsletter and Journal 1964–2004 (link)
Carleen Hutchins Papers 1900–2010 (link)

  Stanford Libraries

Aeolian Company Ledger Books 1905-1930 (organs)

  Lotta Van Buren (restorer, revivalist) -- Brigham Young University

  Resource Name

  Dissertations in Edinburgh University Research Archives (search title or author here)

Applegate, Brian Charles, "Rise and fall of iconic guitar tonewoods and evaluation of alternative species" (link)
Archibald, Paul, "Construction of, and performance on, the early drum kit" (link)
Bento, Pedro; Branco Dos Santos Bento, Pedro, "Harpsichord : its timbre, its tuning process, and their interrelations" (link)
Deters, Sarah Katherine, "Impact of the Second World War on the British piano industry" (link)
Durkin, Rachael  "History and development of the viola d'amore" -
Harrison-Harsley, Reginald Langford, "Physical modelling of brass instruments using finite-difference time-domain methods" (link)
Hill, Matthew William, "George Beauchamp and the rise of the electric guitar up to 1939" (link)
Jenkins, David, "Woodwind instruments in France, 1690-1750: their makers, theoreticians, and music" (link)
Latcham, Michael, "Stringing, scaling and pitch of pianos built in the Viennese and South German traditions 1780 - 1820" (link)
Loomis, Karen Ann, "Organology of the Queen Mary and Lamont harps" (link)
Martin, Darryl, "English Virginal" (link)
Mitroulia, Evgenia, "Adolphe Sax’s brasswind production with a focus on saxhorns and related instruments" (link)
Mole, Peter Geoffrey, "The English Spinet with particular reference to The Schools of Keene and Hitchcock" (link)
Norman, Lisa, "Integrated approach to the analysis of eighteenth-century horns" (link)
O'Brien, George Grant, "Ruckers: a harpsichord and virginal building tradition" (link)
Peppers, Emily, "Introduction of the viol into sixteenth-century France: perspectives on the cultural integration of musical instruments" (link)
Piddocke, Melanie, "Theodor Lotz: a biographical and organological study" (link)
Poulopoulos, Panagiotis, "The Guittar in the British Isles, 1750-1810" (link)
Santa Maria Bouquet, Jonathan, "Reconstructing a lute by Sixtus Rauwolf " (link)
Smith, Poppy Eleanor Win, "History and use of the claviorgan" -
Sugimoto, Hayato, "Harp lutes in Britain, 1800-1830: study of the inventor, Edward Light and his instruments" (link)
Wheeldon, Daniel, "Historical analysis and remaking of two German keyed guitars from the Romantic period using traditional and digital technologies" (link)
Whitehead, Lance, "Clavichords of Hieronymus and Johann Hass" (link)
Yannacopoulou, Joséphine, "A no-longer extant instrument: a study of the medieval viol" (link)

  Resource Name

  RILM Abstracts of Music Literature

  MusiXplora: A Digital Organology Initiative of the University of Leipzig, Music Instrumenten Museum

  Digital Organology — University of Leipzig; Grassi Museum

  Resource Name

  Journal of the American Musical Instrument Society

  Galpin Society Journal

  Historic Brass Society Journal

  Harpsichord & Fortepiano Magazine

  Early Keyboard Journal

  The Tracker – Journal of the Organ Historical Society (US)

  Resource Name

  American Musical Instrument Society

  Historic Brass Society

  British Harpsichord Society

  Catgut Acoustical Society

  CIMCIM

  Centre Sébastien Erard

  Galpin Society

  Historical Harp Society

  International Horn Society

  Lute Society of America

  International Double Reed Society

  Reed Organ Society

  Viola da Gamba Society of America

  Violin Society of America