Wikipedia has been my inspiration for simplifying the problem of indexing and annotation through wiki-style markup. The double-brace syntax for creating hyperlinks is incredibly easy to use — put braces around a phrase and it becomes a hyperlink. Add a pipe in the middle and you can differentiate the link target from the hyperlinked text.
The "what links here" feature is an obvious mechanism for turning online annotations into an index. Hotlink a proper name in the transcribed text to an article on the subject, and that reference is recorded in the RDBMS. It can then be used for showing what contexts that name appears in, suggesting similar hotlinks in new transcriptions, graphing distributions of people and subjects through the work, and generating a print index.