Direct purchase using PayPal ($150 only per license)!FREE DEMO version of the tool is available here.
Update (03/08/2017): A new feature added to this tool, by popular demand... It's now possible to select which pages to add the watermark to. The options are:

• All pages
• Odd Pages (1, 3, 5, 7, etc.)
• Even pages (2, 4, 6, 8, etc.)
• Custom range: You can specify the exact page numbers (or ranges).
  For example: "1-3, 5, 10, 21-57"

The demo version of the tool also includes this functionality, but it will only process the first 3 pages in the selected range.

The new application window now looks like this:

Update (18/03/2017): Yet more new features added to this tool! (and the price is the same...)
It is now possible to specify any rotation angle you wish for the watermark text, not just 0, 45, or -45 degrees.
Also, it's now possible to select the font used for your watermark, either Helvetica, Courier or Times-Roman.

The tool now looks like this:

Update (25/01/2017): Now it's possible to set the font size of the watermark directly in the tool (including the option for automatic font size).
I've also improved the mechanism that calculates the location of the watermark, so it works with landscape pages (or any other dimensions) just as well as with portrait ones.

Update (03/06/2014): Now available is a free demo version of this tool that you can try out before purchasing the full version. The demo version will process only one file at a time, and use only the first 3 items in the list for the watermarks, but it's fully functional beyond that.

This tool is very similar to my script that batch watermarks PDF files, but it is much more powerful. First of all, it is a standalone tool, so you don't need Acrobat to use it, and it can process many more files, and much faster, than a script. In addition, this tool can be used to automatically secure the files with a password to limit the users' ability to edit them. For example, let's say we want to watermark this movie script:

(click to enlarge)

So we run the tool and make our selections: the input file, the names list file (a simple text file), the output folder (where the watermarked copies will be saved), how the watermark text should look like, the file name pattern for the generated files, and whether or not we want to secure those files:

The tool's main window

If we selected to encrypt the files this window will pop open:

And the results will look like this (this is just one of the files generated, of course):

(click to enlarge)

Notice the "(SECURED)" text in the title, which means the file can't be easily edited by the reader.

‍