If you are researching sources, be it written or image sources, on the internet or in real physical publications, you will have run into the how-to-find-stuff problem: Some things are very easy to find, as they are quite prominent. So everybody finds them, and everybody knows them.
Then, of course, these things get cited, and linked to, and re-published, which makes them even easier to find. The books less looked at, the sites less often linked to? Not so visible. Or, as digitizedmedievalmanuscripts.org puts it:
Finding digitized medieval manuscripts is not an easy task: the most prominent libraries are easily found and pinpointed on the maps. Problems arise for all the other digitized libraries that are not discoverable through search engines for many reasons (the website is not optimized or not accessible by crawlers and doesn't appear on web searches, the library is in a language different from English only, or, more in general, the website is difficult to access due to poor web design).
That, of course, is not only true for manuscripts, but DMMapp collects digitised medieval manuscript libraries. There's a long list of libraries that have manuscripts digitised and online, for free - so if you are looking for some things less often looked at... look no further. (Or do, and make sure to tell them about the library if it's not yet in the list.)
Additionally, here's my list of manuscript digitisations, accumulated over the years:
The Bibliothèque Numérique de Lyon has 55 digitised manuscripts in its collection, dating to the 5th to 10th century.
The Book of Kells is online, here's the direct link to the digital book.
The Bamberger Staatsbibliothek offers the digitised Bamberger Apokalypse, dating to the early 11th century.
More old manuscripts, all digitised, can be found in the Virtual Library of Lauresham. The monastery in Lorsch once, in the Middle Ages, had a large number of books and was quite famous. It's not possible to bring the books back to Lorsch in reality, due to a number of reasons, but digitisation of manuscripts allows a virtual reconstruction of the medieval library - which is free to access.
Folgerpedia's digital resources. Folger is the world's largest Shakespeare collection, and you can explore a lot of related topics there as well.
EMMO - Early Modern Manuscripts Online - here you can browse all kinds of different transcribed books, for instance.
Searchable topics of the illustrations of the Maciejowski Bible can be found on this website and this one. The full digitised bible is available online as well, at the Morgan Library website.
You can search the catalogue of Western manuscripts from the Bodleian Libraries plus some Oxford colleges at this site here.
An overview of a number of medieval bestiaries, together with introductory texts, can be found at The Medieval Bestiary. Even better: You get a list of beasts and information about them, their allegories, sources for the things found in the medieval bestiaries, and a gallery with images of these individual beasties, so if you are looking for information about how a specific animal was seen and portrayed in medieval times, this place is a perfect start for your search.
e-codices is aiming to make all the medieval manuscripts in Switzerland available as digitised images - more than 2000 documents are already online.
An annotated list of manuscripts with images regarding clothing can be found on the Wienische Handwerksliute site. Annotations and list are in German.
Die Hausbücher der Nürnberger Zwölfbrüderstiftung are also available online, with possibilities of searching for items or jobs. There is even an English search helper.
The National Library of the Netherlands has an Illuminated Manuscripts database, in English and searchable.
Individual manuscripts are also available in the Cambridge University Library, among them a copy of the Gutenberg Bible, a 13th century Life of Edward the Confessor and a tenth-century Gospel book.
More individual manuscripts are in the Digital Collection of the Württembergische Landesbibliothek Stuttgart.
Heinrich-Heine Uni Düsseldorf has a digital catalogue where you can browse individual manuscripts.
Badische Landesbibliothek Karlsruhe, Manuscript Collection.
Uni Darmstadt, Manuscript Collection.
Handschriftensammlung St. Matthias in Trier
Individual manuscripts can also be found at the British Library in their Turning the Pages section. They include the Luttrell Psalter, the Bedford hours, a Medieval Bestiary and the Sherborne Missal. No image search though, and you really have to leaf through the books.
The Gebetbuch Karls des Kahlen, a prayer book dating to the 9th century.
The Utrecht Psalter, dated to 820-830. There's also a newer, annotated version, where you can get exact inforamtion about which bit of the illustrations corresponds to which bit of the text. No searching for picture contents, though, in either version.
The Harry Ransom center database is called "image database", but is more a manuscript list - texts or titles are in the database, but not detailed image contents. Oldest MS is the Tegernsee Miscellany from around 1000. If there is a digital facsimile available, you can download it as pdf, no previews of the MSS online.