KonaPDF will work on a folder of aliases to Quark or InDesign documents scattered across a number of folders. It will ignore any files in a folder that are not Quark or InDesign documents, nor will it process any files in subfolders.

Once you have your output folder full of PDF files, you might want to combine them into a single PDF, especially if you need to pass on a low-resolution PDF of the entire job to a client, whether by email or FTP.

That's a laborious task in Acrobat, bringing in each page manually and saving the final PDF.

A utility called PDFLab written by Fabien Conus will merge a collection of PDFs into one overall PDF file. It has drag-and-drop capability so it's easy to use.

You can operate the KonaPDF programs through a hotkey from the keyboard by using FastScripts Lite, a free replacement for Apple's own Applescript Menu, and much more powerful.

Hikona
It is always wise to pre-flight Quark documents before outputting PDFs to catch errors (eg RGB images, font substitution etc). When using Hikona to output final, high resolution PDFs ALWAYS check or pre-flight the resulting PDFs. Enfocus offers pre-flight solutions. At a minimum, open up the PDFs created by Hikona in Acrobat and check them at a view of 300-400% and with Overprint Preview option checked (in the Advanced menu).