I recently had the need to merge some PDF scans into a single document. Since I use Ubuntu as my primary workstation and network storage machine- I wanted to work out a solution there (plus I could script it for future use if needed.
The tool to use is Ghostscript. On my fairly stock install, I did not have to install anything.
Here is a command example to combine three PDF files into one:
docs> gs -q -sPAPERSIZE=letter -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile=outfile.pdf infile01.pdf infile02.pdf infile03.pdf
The combined file is even smaller than the combined size of the input file, which is great.