Transcripts tend to be useful for printing, for editing, and for gaining insight by the commentary or annotation that usually accompanies a simple reproduction. Unfortunately, the nature of a transcription is that often a transcriber will have two possible interpretations for a single hand-written word on a manuscript, and will have to choose one of the two. Sometimes a transcriber does not even see more than one possibility.
Therefore, keep in mind that transcriptions are colored by the view of the scholarly editor. It is good to use more than one edition of any piece of literature that you are working on--in fact, it is considered good scholarship to do so.
The Rossell Hope Robbins Library
This library hosts many texts divided into different projects which are accompanied by graphics and criticism, with introductions to the works. These projects include The Camelot Project (on Arthurian studies), The Robin Hood Project, The Medieval Alexander Project (about Alexander the Great during the Middle Ages), and TEAMS Middle English Texts (TEAMS is The Consortium for the Teaching of the Middle Ages; there are a variety of texts here).
The Christian Classics Ethereal Library
This site provides a basic introduction to many Western religious texts, but the real unique thing about this site is that you can download texts in formats that are supported by iPods, palm pilots, and simple text-readers for easy transport on electronic devices. There is no annotation or commentary, but there is author information available on most texts.
Boccaccio’s “Decameron” is a very long work in Italian, but has been translated and transcribed here for the benefit of student. It is accompanied by what the authors call “a growing hypermedia archive of materials dedicated to Boccaccio’s masterpiece”. There are articles on history, society, religion, the arts, the plague, and numerous other resources.
The Luminarium: Anthology of Middle English Literature (1350-1485)
This anthology has a variety of transcriptions and is organised by author. Accompanying the works of these authors are criticism tailored to the specific work or author, links to discussion forums, bookstores that sell these works, and other options--not all of these options accompany every work, but each work is provided amply for an introduction.