Since it's not terribly hard to use Zotero to download lots of PDFs concerning Ulysses from common databases (JSTOR, Project Muse), it'd be relatively easy to text-match between our Ulysses text and some of the more well-known critical articles.
We could even match on books by scripting something to query Google Books or Hathi Trust for every five-gram in the novel. The process would take a while, but it'd be worth it.
There are also the "popular passages" listed on the Google Books "About this Book" pages, which link to other works that cite those passages. The only issue here is that the number of passages is limited to about 12.
I'm looking into how best to do this in TEI. This page describes citation formats. It looks like Zotero can export to TEI, so that really simplifies the process.
My guess now is that the text could have something like this in it:
<note target="#gilbert1982">Gilbert calls this word "eminently Joycean."</note> which would then refer to a
bibliography.xml which would contain a TEI bibliography.
Input and opinions on this front would be very welcome.