###While this script does concatenate pdf files, I haven't yet figured out in which order it does so. On a sample of 19 pdf files, logically named 01something.pdf, 02something.pdf, 03something.pdf, etc. the order of the merged product seemed almost random...
...from Tiger onwards, OSX ships with a Python script that concatenates pdf files (merges them together). The script is already executable, and Python is pre-installed on OS X, so all you need to do is point it at your pdf files and run
"/System/Library/Automator/Combine PDF Pages.action/Contents/Resources/join.py" -o PATH/TO/YOUR/MERGED/FILE.pdf /PATH/TO/ORIGINAL/1.pdf /PATH/TO/ANOTHER/2.pdf /PATH/TO/A/WHOLE/DIR/*.pdf
I prefer putting the link in /usr/local/bin, as it is in the $PATH and therefore I can run the command from anywhere. To set up the link, you need to navigate to the directory where you want the link.
cd /usr/local/bin
sudo ln "/System/Library/Automator/Combine PDF Pages.action/Contents/Resources/join.py" PDFconcat
Terminal will ask you for your password (you need Admin rights to do this). After the command is run, you will be able to concatenate PDF files anywhere on Terminal by typing
PDFconcat -o PATH/TO/YOUR/MERGED/FILE.pdf /PATH/TO/ORIGINAL/1.pdf /PATH/TO/ANOTHER/2.pdf /PATH/TO/A/WHOLE/DIR/*.pdf
You can even pass a ‘shuffle’ argument to make the script take one page per document in turn instead:
PDFconcat -s -o PATH/TO/YOUR/MERGED/FILE.pdf /PATH/TO/DIR/*.pdf