A good transcription is more than just a faithful translation of pen-strokes to a digital, print-style alphabet. It has to expand whatever has been unduly abbreviated, convert shorthand to conventional orthography, provide guesses for illegible text (with the reasoning for the guess explained) and smooth over obvious errors - such as repeated words - by the scribe.
The typography should distinguish the words and letters that were unarguably in the original document from those that the transcriber has "read into" the document. Traditionally this is an either-or affair.
Major transcription projects such as the Papers of George Washington encourage their transcribers to "silently" expand shorthands that indicate a double letter, an incomplete word, a contraction or a misspelled word, but to enclose doubtful words in brackets. This practice— the two-way choice between original running text or editorial inserts— is dictated by the print form. It is a practice that makes the work of transcribing harder than it should be, because many transcribers are not so confident about their translations.
A digital transcript allows a wider range of presentations and therefore greater leeway. Suppose, for example, that a transcriber wants, for the sake of veracity, to also record the precise abbreviations found in the manuscript. The Text Encoding Initiative's recommendation on transcriptions suggests enclosing an expanded word in tags like this:
with the abbreviation added as an attribute like this:
This can be mapped quite well onto an HTML tag, for example:
<span class="expan" title="defti">defuncti
The hidden text will be visible as a tool-tip if the web user places the mouse cursor over the word, as in this example:
defuncti. Try it.
This simple technique is explained in detail in the section of this style guide dealing with glosses. If the tool-tip has to contain unusual or differently sized characters, or a translation of a longer passage in Latin, use this style guide's technique for pop-up footnotes.