Pdfunite

pdfunite from the poppler package is a useful cli tool which allows you to merge pdfs. The below wrapper script is useful e.g as a custom action in Thunar:

#!/bin/bash
# $HOME/bin/merge-pdfs.sh
echo "Merging pdfs:"
pdfs=""
for file in $*; do
   echo "    $file"
   pdfs="$pdfs "$file
done
echo ""
read -p "Output file name [merge.pdf]: " result
outfilename=${result:-merge.pdf}
echo ""
pdfunite $pdfs $outfilename && echo "Merged to $outfilename"
sleep 1
evince $outfilename

The corresponding command for a Thunar custom action (mapped to pdf files) would be

terminator -e "$HOME/bin/merge-pdfs.sh %F"