General
Music Theory
Ethnomusicology
Musicology
Musical Acoustics and Psychoacoustics

General

Worldwide Internet Music Resources---a large and well-kept directory from the University of Indiana.
Music Resources---another huge directory, from the Sibelius Academy.
Internet Resources for Music Scholars---another, with a scholarly focus, from Harvard University.
Newsgroups and Mailing Lists---probably the best list of lists of musical mailing lists and Usenet News faqs.
CAIRSS---a bibliographic database of music research literature.
Grove---Their New Grove Dictionary of Music and Musicians and other dictionaries claim to be the best general references, and probably are, but they have been severely limited by their Eurocentric, art music perspective.  The new edition and online subscription service, however, promise improvements.
The Garland Encyclopedia of World Music---looks dazzling, on the other hand. We haven't yet had the chance to read it, but we're very eager to. It may be bought here.

Music Theory

There are a lot of "EZ" music theory sites that can get beginners off to a bad start. For anyone, beginner or trained theorist looking for a clear exposition of Western theory, we recommend Ralph Turek's excellent text, Elements of Music: Concepts and Applications (volume 1, volume 2). For an interesting contrast, see Richard Sorce's Music Theory for the Music Professional: A Comparison of Common-Practice & Popular Genres and for jazz, see Mark Levine's The Jazz Theory Book.  One exceptional webpage might be the Gems of Compositional Wisdom, some interesting practical insights hiding behind a grandiose title (not that we at the OI think that grandeur is anything of which to be ashamed).  A Practical Guide to Musical Composition is in a similar vein; it's interesting to compare them with the advice of Brahms. Larry Solomon also has some useful information for Western composers.  If you must have a basic online reference, try Star Theory or this or this.

Most sources have an almost completely Western bias:
The Society for Music Theory---a large scholarly organization.
Texas Institute of Theory---a shameful masquerade, in our opinion.
The Journal of Music Theory---from Yale.
Music Theory Online---an online journal from the Society for Music Theory.

Some interesting work:
Michael Keith, From Polychords to Polya: Adventures in Musical Combinatorics---an interesting examination of music theory with combinatorial mathematics.
Guide to Shenkerian Analysis---an excellent online introduction to Schenker's method.
Bimodalism---the harmonic system of Enrique Ubieta.
Cognitive Constraints on Compositional Systems---a surprisingly good introduction to Fred Lerdahl and cognitive music theory. Lerdahl and Jackendoff's book, A Generative Theory of Tonal Music, has become a classic.
Polytonics---the harmonic system of William Matthew Beachy.
The Schillinger System---devoted to the work of Joseph Schillinger.
Tone Clock---Theo Hoogstins on Peter Schat's harmonic system.
A Theory on Open Modality---the harmonic system of Emery Szasz.
Hans Straub's MaMuTh Page---dedicated to Mathematical Music Theory.
An essay on patterns in musical composition---a good essay on mathematics in music theory from Bill Hammel, who has several others here.
MusicMedia Science---important work in performance analysis and a forum for fundamental research in music.

Ethnomusicology

Books:
The Garland Encyclopedia of World Music---a massive reference covering all areas, eras and genres. It may be bought here.
Porter, The World's Music (Garland Encyclopedia of World Music, Volume 10)---an essential reference.
Reck, Music of the Whole Earth---an excellent popular treatment, many will find it broadening.
Titon, Fujie and Locke (editors), Worlds of Music: An Introduction to the Music of the World's Peoples---a good introductory text.
Nettl (Editor), Excursions in World Music, 2nd edition---an excellent, readable introduction, with CD enhancement.
Nettl, Study of Ethnomusicology---an introduction by a giant.
Kunst, Ethnomusicology---a classic introduction.
May and Hood, Musics of Many Cultures: An Introduction---twenty essays on non-Western musics.
Myers and Sadie (editors), Ethnomusicology : Historical and Regional Studies---a popular sourcebook.
Shelemay (editor), Ethnomusicology: History, Definitions, and Scope: A Core Collection of Scholarly Articles---this anthology provides a good historical overview.
Nettl, et al., Comparative Musicology and Anthropology of Music: Essays on the History of Ethnomusicology---this anthology provides a critique of the discipline.
Sullivan (Editor), Enchanting Powers: Music in the World's Religions---this anthology adresses a fascinating set of genres.
Nettl and Russell (Editors), In the Course of Performance: Studies in the World of Musical Improvisation---an interesting anthology on systems of improvisation.
Kartomi, On Concepts and Classifications of Musical Instruments---a synthesis of trational organologies.
The Origins of Music---a interdisciplinary anthology and an important first step in the field. Should we greet the birth of evolutionary biomusicology with elation or suspicion?

Directories:
Ethnomusicology, Folk Music, and World Music---a large directory from the University of Washington.
Ethnomusicology Sources on the Internet---a large directory.
Online Sources for Ethnomusicological Information---another resource guide.
Ethnomusicology Bibliographic Guide---a good, basic bibliography, but it needs an update.
guide to programs---a guide to academic programs in ethnomusicology.
Folklore---Library of Congress Gopher.

Societies:
The International Council for Traditional Music---a UNESCO NGO with study groups, colloquia, etc.
The Society for Ethnomusicology---a large scholarly organization.
The European Seminar in Ethnomusicology---holds annual conferences.
The Society for Asian Music---featuring their journal.
Music Research Institute---focused on contemporary and cross-cultural issues.

Publications:
Ethnomusicology OnLine---an online journal.
Music & Anthropology---an online journal with an emphasis on the Mediterranean.
Trans---an online interdisciplinary journal.
Ethnomusicology Research Digest---a mailing list from the University of Maryland.
Cognitive Ethnomusicology Email List---for those whose research interests combine ethnomusicology and cognitive science.
Yearbook for Traditional Music---a journal from Columbia University.
The British Journal of Ethnomusicology---from the British Forum for Ethnomusicology.
The Pacific Review of Ethnomusicology---an occasional (not less than once a year) publication from UCLA.
Journal of the Society for Asian Music---covering the whole of Asia.
Musical Traditions---an online folk music magazine with a lot of material.

Archives:
Resources on Early Recordings---a variety of resources, including early ethnographic recordings.
Archive of World Music---a large collection at Harvard University.
The Archives of Traditional Music---the largest university archives in the United States, at Indiana University.
International Music Collection---of the British Library National Sound Archive.

Other sources:
Speakeasy World Music Pages---some interesting articles on rhythm.
AudioWorks Ltd.---produces audio-to-MIDI converters.
Wildcat Canyon Software---produces audio-to-MIDI converters.
AmazingMIDI---an audio-to-MIDI converter.
Note Chaser---transcription software featuring visual displays.
Woodshed Home---software that slows down audio without changing pitch.
Seventh String Software---software that slows down audio without changing pitch.
(Note: a good sound editor, such as CoolEdit can be useful for transcription.)
 

Musicology

Unfortunately, musicology is not the science of music it set out to be; it tends to focus on the minutia of Western art music of the common-practice era.
Cockerell and Miller, History of Western Music, 5th edition---a clear first text.
Grout and Palisca, A History of Western Music, 5th edition---a standard reference text.
Lang, Music in Western Civilization---a well-loved classic. enormous.
Bergeron and Bohlman (Editors), Disciplining Music: Musicology and Its Canons---arguments for a broader music, a position toward which the Institute is highly sympathetic.
Chadabe, Electronic Sound: The Past and Promise of Electronic Music---the definitive history of the subject.
Chanan, Repeated Takes: A Short History of Recording and Its Effects on Music---a fascinating study.
Theberge, Any Sound You Can Imagine: Making Music/Consuming Technology (Music/Culture)---an interesting study of the sociology of music technology.
Cadwallader and Gagne, Analysis of Tonal Music: A Schenkerian Approach---probably the best guide to Shenkerian analysis.
Vander Weg, Serial Music: A Research and Information Guide---comprehensive and up-to-date.
Castine, Set Theory Objects: Abstractions for Computer-Aided Analysis and Composition of Serial and Atonal Music---fascinating to those of us interested in object-oriented representations of musical ideas.
Hewlett and Selfridge-Field (Editors), Melodic Similarity: Concepts, Procedures, and Applications---excellent work in musicological computing.

The American Musicological Society---a large scholarly organization.
Journal of the American Musicological Society---and its journal.
South African Journal of Musicology---from the Musicological Society of Southern Africa.
Sites of Interest to Musicologists---and many others.
Music History Resources---a good outline of Western theory.
Unknown Composers---champion an unknown and Fame with her fickle trumpet will bless you.
The Music Performance Research Centre---an archive of sound documents at the Barbican Centre, London.
The Petrucci Project---a noble effort to digitize out-of-print music; we encourage you to volunteer.
International Association for the Study of Popular Music---a large scholarly organization.
Hypermusic---histories of jazz and classical music.

Cognitive Musicology:
Tabor (Editor), Otto Laske: Navigating New Musical Horizons---compositional practice and musicological research using computers with ethnographic considerations.
Narmour, The Analysis and Cognition of Basic Melodic Structures: The Implication-Realization Model---and (see below):
Narmour, The Analysis and Cognition of Melodic Complexity: The Implication-Realization Model---fascinating, these two books present a comprehensive theory of melody.
Lerdahl and Jackendoff, A Generative Theory of Tonal Music---a classic exposition of the cognitive approach.
Lerdahl, Tonal Pitch Space---eagerly awaited.
Leman (Editor), Music, Gestalt, and Computing: Studies in Cognitive and Systematic Musicology---
Desain and Honing, Music, Mind, and Machine: Studies in Computer Music, Music Cognition, and Artificial Intelligence---
The Institute for Music Research---concentrates on music technology, music psychology and their integration.
The European Society for the Cognitive Sciences of Music---a large scholarly organization.
MuSICA---research on music as related to behavior, the brain and allied fields.
Music, Mind, Machine ---at the University of Nijmegen.
Music Cognition---at the Ohio State University.
Cognitive Musicology---connectionism, physicalism and representation at the Universities of Jyväskylä and Helsinki.

Musical Acoustics and Psychoacoustics

for Musical Acoustics in general:
Fletcher and Rossing, The Physics of Musical Instruments, 2nd edition---a solid first text; well done.
Benade, Fundamentals of Musical Acoustics---an excellent introduction, but light on mathematics.
Roederer, The Physics and Psychophysics of Music: An Introduction, 3rd edition---another good introduction with light mathematics.
Hall, Musical Acoustics---a first text.
Benade, Horns, Strings, and Harmony---a popular treatment by a major name in acoustics.
Olson, Music, Physics and Engineering---another good popular introduction.
Helmholtz, On the Sensations of Tone---this nineteenth century classic would be of historical interest only, if it were not for the extensive appendices by Ellis.
Nederveen, Acoustical Aspects of Woodwind Instruments---useful for makers and synthesists.
Cremer, Physics of the Violin---useful for makers and synthesists.
Rossing, Science of Percussion Instruments---eagerly awaited.
Embleton (Editor), Aip Handbook of Condenser Microphones: Theory, Calibration, and Measurements---for acoustical research.
Physics of Sound---notes from a course at the Australian National University.

for Psychoacoustics:
Deutsch (editor), The Psychology of Music, 2nd edition---massive and seminal, extraordinary coverage.
Moore, An Introduction to the Psychology of Hearing, 4th edition---a solid first text.
Warren, Auditory Perception: A New Analysis and Synthesis---a popular first text, with a CD of examples.
Cook (editor), Music, Cognition, and Computerized Sound: An Introduction to Psychoacoustics---an excellent place for the computer musician to start.
Hartmann, Signals, Sound, and Sensation (Modern Acoustics and Signal Processing)---a useful second text, focusing on the mathematics of signals.
Zwicker, et al., Psychoacoustics : Facts and Models---for advanced students, a source for many practical details of models and experimental design.
Bregman, Auditory Scene Analysis: Perceptual Organization of Sound---an important exposition of modern theories concerning complex auditory perception; see also Rosenthal and Okuno (Editors), Computational Auditory Scene Analysis.
Blauert, Spatial Hearing: The Psychophysics of Human Sound Localization, Revised edition---essential for researchers in localization, spatialization and three-dimensional sound of every kind.
Trance Balinese Barong, Gnawa Music of Morocco, Zkir from Chinese Turkestan (The Musica Expeditions Series/Book and CD)---interesting examples of trance-inducing music.

Tinnitus FAQ---if you suffer from a constant ringing in the ears.
Music Experiment Development System (MEDS)---software for developing and running multimedia perception experiments.
A Basic Bibliography for Sonic Studies---from the World Forum for Acoustic Ecology.
Books & Articles on Acoustics---another good, basic bibliography.
The International Commission for Acoustics---a large scholarly organization.
Institute of Acoustics---a large scholarly organization in the UK.
The Acoustical Society of America---a large scholarly organization.
Catgut Acoustical Society---an organization devoted to musical acoustics and instrument building, especially violins.
Audio Engineering Society---publishes an important journal.
Institute for Psychoacoustics and Electronic Music---a Belgian organization.
Musical Illusions and Paradoxes---a CD illustrating the fascinating work of Diana Deutsch.
Archeoacoustics---unintentional sound recordings of great antiquity.
The Acheoacoustic Player---an attempt at recovering ancient sounds.
Fish Acoustics---delightful.

The general reference stacks.