EM has started work on adding reference material for all the classical allusions etc. in the Sonnet (1621 version). I've created a file called references.xml, which EM is editing; it has a separate <div> for each "topic", with a unique @xml:id attribute. References in the text are linked like this:

<ref type="reference" target="references.xml#topicId">blah</ref>

Once we have a fully marked-up document, I'll be able to write the handling code (intercepting handling of existing <ref> elements, which have no @type attribute, and which handle cross-references in editorial notes.