The best tool I have found is ConnectedText. It's not perfect, but it does the job. It's basically a full-featured wiki in a desktop application, with alright query capabilities baked into the markup language. Also a really good category system. I use it pretty much exactly like your boss used his "master file".

For example I have a page called "Reading Log" whose content is:

  [[$SUMMARY:[$PR Read <> ""]|-Read|Rating|Author|Type]]

This is a query that finds any pages with the "Read" property and then produces a table with all the stuff I have read, in descending order of reading date, along with the rest of the properties listed. Unfortunately the query language is not particularly powerful, some things I've wanted to do have not been possible.