Important update: Unfortunately, Adobe have been gradually removing the support for DB connectivity in Acrobat (except for forms created using LiveCycle Designer). As of Acrobat XI this functionality is completely gone.
I've recently developed a set that allows you to connect your PDF to a local or networked database.
It's possible to copy highlighted text, bookmarks, form field values, etc. from your PDF directly into a database table, such as Access databases. It's even possible to access the database from your file and populate fields or create bookmarks based on data read from it. The possibilities are endless.
NEW: You can now download a working example that shows how this tool actually works.
It contains a sample database and a PDF that reads the data off of this database and uses it to populate the form fields in it. The full set of tools is, of course, able to both read and write data off the database.
You can download the sample files from here.
This is a really powerful set of tools. If you're interested in purchasing it, contact me directly.