Athens, National Library of Greece
Sakkeliōn, Iōannēs = Σακκελίων, Ιωάννης and Σακκελίων, Αλκιβιάδης Ι. Κατάλογος χειρογράφων της Εθνικης Βιβλιοθήκης της Ελλάδος. Athens: Εθνικό Τυπογραφείον και Λιθογραφείον, 1892.
Politēs, Linos = Πολίτης, Λίνος. Κατάλογος των χειρογράφων της Εθνικής Βιβλιοθήκης της Ελλάδος: αρ. 1857-2500. (Πραγματείαι της Ακαδημίας Αθηνών, 54). Athens: Academy of Athens, 1991.
The website of the Library has a collection of digitized printed catalogs and a manuscript search engine.
Athens, Benaki Museum
Athos
See “Mount Athos” below.
Baltimore, MD, Walters Art Gallery
Online (Harvard ID required)
Basel, Universitätsbibliothek
Berlin, Staatsbibliothek – Preussischer Kulturbesitz
Besançon, Bibliotheque de l’Université de Franche-Comté
Bologne, Biblioteca Universitaria
Budapest, ELTE University Library (Eötvös Loránd Tudományegyetem)
Catalogus Codicum Bibliothecae Universitatis R(egiae) Scientiarum Budapestinensis. Budapest: Typographiae Universitatis Reg. Scientiarum Budapestinensis [nunc Eötvös Loránd Tudományegyetem], 1881. (Online: semel et bis.)
Cambridge (UK), Cambridge University Library
Cambridge (UK), Trinity College Library
Cambridge, MA, Houghton Library
Copenhagen, Kongelige Bibliotek
Dresden, Sächsische Landesbibliothek
Dublin, Trinity College Library
Erfurt, Bibliotheca Amploniana
Erlangen, Universitätsbibliothek
Florence, Biblioteca Medicea Laurenziana
Bandini, Angelo Maria. Catalogus codicum manuscriptorum bibliothecae Mediceae Laurentianae varia continens opera Graecorum patrum… 3 vols. Florence: Typis Caesareis, 1764-1770.
Volume 1 (also here); Volume 2; Volume 3 (also here)
The website of the Library has a manuscript search engine with full digital reproductions and bibliography (including cross-references).
Florence, Biblioteca Marucelliana
Florence, Biblioteca Riccardiana
Geneva, City Library
Glasgow, University of Glasgow Library
Göttingen, Niedersächsiche Staats- und Universitätsbibliothek
Grottaferrata, Biblioteca
Rocchi, Antonio. Codices Cryptenses seu abbatiae Cryptae Ferratae in Tusculano digesti et illustrati. Typis Abbatiae Cryptae Ferratae, 1883.
Hamburg, Staats- und Universitätsbibliothek
Heidelberg, Universitätsbibliothek
Istanbul, Patriarchate Library
Istanbul, Topkapi Palace
Jerusalem, Greek Orthodox Patriarchate
Papadopoulos-Kerameus, Athanasios = Παπαδόπουλος-Κεραμεύς, Αθανάσιος. Ιεροσολυμιτική βιβλιοθήκη: ήτοι κατάλογος των εν ταις βιβλιοθήκαις του αγιοτάτου αποστολικού τε και καθολικού ορθοδόξου πατριαρχικού θρόνου των Ιεροσολύμων και πάσης Παλαιστίνης αποκειμένων ελληνικών κωδίκων. 5 vols. Εν Πετρουπόλει: Εκ του τυπογραφείου Β. Κιρσπάουμ, 1891-1915.
Collection of the Μετόχιον Παναγίου Τάφου, previously in Constantinople, now in the National Library of Greece:
Karlsruhe, Badische Landesbibliothek
Leiden, Rijksuniversiteit
Meyier, Karel Adriaan de. Codices Vossiani Graeci et miscellanei. Lugduni Batavorum: Bibliotheca Universitatis, 1955.
Meyier, Karel Adriaan de. Codices bibliothecae publicae Graeci. Lugduni Batavorum: Bibliotheca Universitatis, 1965.
Leipzig, Universitätsbibliothek
London, British Library
London, Wellcome Library
Madrid, Biblioteca Nacional de España
Iriarte, Juan. Regiae bibliothecae Matritensis codices Graeci manuscripti… E typographia Antonii Perez de Soto, 1769. (Online)
Andrés, Gregorio de. Catálogo de los codices griegos de la Biblioteca Nacional. Madrid: Ministerio de Cultura, Dirección General del Libro y Bibliotecas, 1987. (Online)
Madrid, El Escorial
Miller, Emmanuel. Catalogue des Manuscrits Grecs de la Bibliothèque de l’Escurial. Paris: Imprimerie Nationale, 1848. (Online)
Revilla, Alejo and Gregorio de Andrés (Martínez). Catálogo de los Códices Griegos de la Biblioteca de El Escorial (3 vols.). Madrid: 1936, 1965, 1968. (Online)
* The Escorial Library have put the whole of Revilla & Andrés’s excellent catalogue online in pdf/aspx format (above), but navigating it can be slightly tricky and deserves comment. It’s in fifteen parts, as follows:
1/15: Vol. 1 (Revilla), pp. i-cxxxv (prologue, corrigenda &c.).
2/15: Vol. 1 (Revilla), pp.001-100 (codd. 1-24 [r.i.1—r.ii.4]).
3/15: Vol. 1 (Revilla), pp.100-200 (codd. 25-58 [r.ii.5—r.iii.24]).
4/15: Vol. 1 (Revilla), pp.201-309 (codd. 59-87 [r.iii.25—σ.ii.7]).
5/15: Vol. 1 (Revilla), pp.310-402 (codd. 88-124 [σ.ii.8—τ.i.4]).
6/15: Vol. 1 (Revilla), pp.404-501 (codd. 125-157 [τ.i.5—τ.i.18]).
7/15: Vol. 1 (Revilla), pp.502-560 (codd. 158-178 [τ.ii.19—τ.iii.18] and indices).
8/15: Vol. 2 (Andrés), pp. i-xvi (prologue) and 001-095 (codd. 179—251 [φ.i.1-υ.i.12]).
9/15: Vol. 2 (Andrés), pp. 096-193 (codd. 252-308 [υ.i.13—y.i.15]).
10/15: Vol. 2 (Andrés), pp.193-282 (codd. 309-372 [y.ii.1—χ.ii.12]).
11/15: Vol. 2 (Andrés), pp. 283-357 (codd. 373-420 [χ.ii.13—χ.iv.25]).
12/15: Vol. 3 (Andrés), pp. 001-119 (codd. 421-503 [ψ.i.1—ω.i.2]).
13/15: Vol. 3 (Andrés), pp. 120-203 (codd. 504-551 [ω.i.3—ω.iii.18]).
14/15: Vol. 3 (Andrés), pp. 204-263 (codd. 552-649 [ω.iii.19—82.vii.22]).
15/15: Vol. 3 (Andrés), pp. 265-368 (indices).
The links from the library website will open as pdf’s in the browser and can be saved as such from there, though this is slow and unstable (prone to crashing). Alternatively, you can right-click the link and save the file (“save link as”) to your computer. This will save your selection as an “ASP” file, which most computers are not by default set up to read; but simply changing the file extension from .aspx to .pdf will make it open up as the familiar Adobe document. (Miller’s catalogue above is older and usually less full, but can often be profitably compared; see bibliography and online resources.)
Messina, Biblioteca Universitaria di Messina
Milan, Biblioteca Ambrosiana
Martini, E. and Bassi, D. Catalogus codicum Graecorum bibliothecae Ambrosianae. (2 vols.) Milan: U. Hoepli, 1906.
The website of the Library has a manuscript search engine with contents and bibliography.
Moscow, Synodal Library [State Historical Museum]
Arhimandrit Vladimir = Архимандрит Владимир. Систематическое описание рукописей Московской Синодальной (Патриаршей) библиотеки. Част I: Рукописи греческие. [A systematic description of the manuscripts of the Synodal (Patriarchal) Library in Moscow. Part 1: Greek manuscripts]. Москва: Синодальная тип., 1894.
Mount Athos [except Great Lavra and Vatopedi Monastery]
Lampros, Spyridοn Paulou. Catalogue of the Greek Manuscripts on Mount Athos. Cambridge: CUP, 1895-1905.
Mount Athos, Vatopedi Monastery
Mount Athos, Great Lavra Monastery
Eustratiades, Sōphronios = Σπυρίδων, μοναχός Λαυριώτης and Ευστρατιάδης, Σωφρόνιος. Κατάλογος των κωδίκων της Μεγίστης Λαύρας (της εν Αγίω Όρει). Paris: Librairie Ancienne Honoré Champion, 1925.
Munich, Bayerische Staatsbibliothek
New Haven, CT, Yale University Medical Library
Palermo, Biblioteca Comunale di Palermo
Paris, Bibliothèque Nationale
Perugia, Biblioteca Comunale
Rome, Biblioteca Angelica
Rome, Biblioteca Vallicelliana
Martini, Emidio. Catalogo di manoscritti greci esistenti nelle biblioteche italiane: Catalogus codicum græcorum qui in Bibliotheca vallicellana Romæ adservantur. Milan: U. Hoepli, 1902.
Strasbourg, Bibliothèque Nationale et Universitaire
Toledo, Biblioteca del Cabildo
Graux. Ch. and Martin, A. Rapport sur une mission en Espagne et en Portugal. Nouvelles archives des missions scientifiques et littéraires 2 (1892), pp. 229-298.
Uppsala, Universitetsbiblioteket
Vatican, Biblioteca Apostolica Vaticana
The catalogs of the main collection (Vaticani graeci) are not accessible online.
Stevenson, Henry M. Codices manuscripti palatini graeci Bibliothecae Vaticanae descripti praeside I. B. cardinali Pitra. Romae: ex Typographeo Vaticano 1885.
Codices Reginenses graeci
Stevenson, Henry M. Codices manuscripti graeci Reginae Svecorum et Pii Pp. II. Bibliothecae Vaticanae descripti praeside I.B. Cardinali Pitra. Romae: Ex Typographeo Vaticano 1888.
Codices Urbinates graeci
Stornajolo, Cosimus. Codices urbinates graeci Bibliothecae Vaticanae, descripti praeside Alfonso cardinali Capecelatro. Romae: ex Typographeo vaticano 1895.
The website of the Library has a search engine with relevant bibliography published in Studi e Testi.
Venice, Biblioteca Nazionale Marciana
Recent catalogs by Elpidio Mioni are not accessible online.
Old catalogs are accessible here:
Fondo antico
Zanetti, 
Antonio Maria and Bongiovanni, Antonio . Graeca D. Marci bibliotheca codicum manu scriptorum per titulos digesta praeside et moderatore Laurentio Theupolo. [Venetiis:] apud Simonem Occhi 1740.
The Biblioteca Digitale Italiana offers access to old hanwritten catalogs.
Vienna, Österreichische Nationalbibliothek
Hunger, Herbert and Kresten, Otto. Katalog der griechischen Handschriften der Österreichischen Nationalbibliothek. 1: Codices historici, codices philosophici et philologici. 2: Codices juridici, codices medici. 3,1: Codices theologici 1-100. 3,2: Codices theologici 101-200. 3,3: Codices theologici 201-337. Wien: Prachner; Hollinek, 1961-1992.
Manuscripts on Microfilm 