From the gs package in Ubuntu:

gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=outputMerged.pdf file1.pdf file2.pdf

jPdf Tweak, the “Swiss Army Knife for PDF files”, is also a great tool and run out of the box with Java but it might be faster just using the above command rather than browsing through jpdftweak’s GUI.