[pdf] How to merge many PDF files into a single one?

You can also use Ghostscript to merge different PDFs. You can even use it to merge a mix of PDFs, PostScript (PS) and EPS into one single output PDF file:

gs \
  -o merged.pdf \
  -sDEVICE=pdfwrite \
  -dPDFSETTINGS=/prepress \
   input_1.pdf \
   input_2.pdf \
   input_3.eps \
   input_4.ps \
   input_5.pdf

However, I agree with other answers: for your use case of merging PDF file types only, pdftk may be the best (and certainly fastest) option.

Update:
If processing time is not the main concern, but if the main concern is file size (or a fine-grained control over certain features of the output file), then the Ghostscript way certainly offers more power to you. To highlight a few of the differences:

  • Ghostscript can 'consolidate' the fonts of the input files which leads to a smaller file size of the output. It also can re-sample images, or scale all pages to a different size, or achieve a controlled color conversion from RGB to CMYK (or vice versa) should you need this (but that will require more CLI options than outlined in above command).
  • pdftk will just concatenate each file, and will not convert any colors. If each of your 16 input PDFs contains 5 subsetted fonts, the resulting output will contain 80 subsetted fonts. The resulting PDF's size is (nearly exactly) the sum of the input file bytes.