I'm recursively going through my XML file to create a table of contents
for a document. I want to be able to link each item on the TOC to the
proper anchor later on the page.

The 'easy' solution would be for me to just store the unique ID stored
in the database for each node within the XML itself, but I was wondering
if there was a solution on the XSL side of things before I recreate the
XML files.

Just use generate-id() - it's guaranteed to return the same value for
the same node for a single transformation run.

So when you pass over your data to create your index, and then when
you pass over it a second time to do the actual transform, as long as
its all done as part of a single transform you can use generate-id()

cheers
andrew