Direct purchase using PayPal ($85 per license)!
A free demo version of this tool that will combine up to two files in each folder can be found here.
This is a new batch tool, so it can only be used in Acrobat Pro.
With this tool you can combine all of the (PDF) files in a folder to a single file (in order!) and have this file saved into the same folder (using the folder's name as the new file name).
New feature: You can now select to automatically create a bookmark pointing to each file in the merged document.
ANOTHER new feature: Now you can also select to create a single, "master" file at the end of the process, which contains all of the processed files, including a bookmark for each folder and file.