pdftk infile1.pdf multibackground infile2.pdf output outfile.pdf
pdfovl is a utility I wrote (actually more like modified) while setting up JoCG when faced with the task of stamping page numbers and volume information on PDF files. This was a frustrating experience and the only suitable software cost hundreds of dollars. I learned that, in the world of PDF processing, a GUI decreases the cost of products and command-line tools are expensive.
I considered asking for a software donation from one of the commercial vendors, but having followed the Linux/Bitkeeper fiasco, I decided that relying on proprietary software for running an open access journal was a bad idea. As a result, I ended up writing a small utility based on iText. Once I found what I needed, it only took about an hour to write. It turns out that this was a useful exercise; iText is a great library and I will probably end up using it for more journal related stuff (page resizing, for example) in the future.
pdfovl takes two PDF files and merges (overlays) them page by page so that the text of both files appears on the same page. The files must have the same number of pages and the same paper size.
If you want to say something nice about pdfovl, you can email me. If you would like to see a feature added, then you have to right to modify the code yourself and add that feature.