pdftk

To merge two pdf files, file1.pdf and file2.pdf:

pdftk file1.pdf file2.pdf cat output mergedfile.pdf

More info available here^{Way Back Machine}.

To install, run:

sudo snap install pdftk

PDF Arranger (install), formerly known as PDF-Shuffler.

If you want a tool with a simple GUI, try pdfarranger. It allows for merging of PDFs as well as rearranging and deleting pages. For batch processing and/or more complicated tasks, pdftk is of course more powerful.

Ghostscript is a package (available by default in Ubuntu) that enables you to view or print PostScript and PDF files to other formats, or to convert those files to other formats.
To use Ghostscript to combine PDF files, type something like the following:

gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -dAutoRotatePages=/None -sOutputFile=finished.pdf  file1.pdf file2.pdf

Here is a brief explanation of the command:

gs         starts the Ghostscript program.
-dBATCH    once Ghostscript processes the PDF files, it should exit.
           If you don't include this option, Ghostscript will just keep running.
-dNOPAUSE  forces Ghostscript to process each page without pausing for user interaction.
-q         stops Ghostscript from displaying messages while it works
-sDEVICE=pdfwrite 
           tells Ghostscript to use its built-in PDF writer to process the files.
-sOutputFile=finished.pdf
           tells Ghostscript to save the combined PDF file with the specified name.
-dAutoRotatePages=/None
           Acrobat Distiller parameter AutoRotatePages controls the automatic orientation selection algorithm: For instance: -dAutoRotatePages=/None or /All or /PageByPage.

Your input files don't even need to be PDF files. You can also use PostScript or EPS files, or any mixture of the three.

There is a lot you can do with Ghostscript. You can read its documentation for more details.

_Source

You also also use pdfunite to merge pdf documents :

pdfunite in-1.pdf in-2.pdf in-n.pdf out.pdf

To install pdfunite if it is not installed already, run:

sudo apt-get install poppler-utils

PDF Chain

A very nice solution is PDFChain. It's GUI is a frontend of PDFTK where you can merge, split or even add some background to your PDF files.

An alternative approach is to use Latex as explained in this post (without root access assuming that you have pdflatex installed): https://tex.stackexchange.com/questions/8662/merge-two-pdf-files-output-by-latex

This is useful in case you do not have the mentioned tools nor root privileges, but you do have pdflatex.

I copy the tex code below to merge file1.pdf and file2.pdf. Create a file called output.tex and put:

\documentclass{article}
\usepackage{pdfpages}
\begin{document}
\includepdf[pages=-]{file1}
\includepdf[pages=-]{file2}
\end{document}

And to compile, simply use: pdflatex output.tex

The merged file will be named as output.pdf.

Give PDFMod a try, it’s from the GNOME project:

https://wiki.gnome.org/Apps/PdfMod

sudo apt install pdfmod

Use pdfsam http://www.pdfsam.org/ it's very good for splitting and merging pdfs

sudo apt install pdfsam

I use pdfseparate to extract specific pages from big pdf file:

pdfseparate -f  156 -l 157 input.pdf  output_%d.pdf 
pdfseparate -f  1   -l 2   input.pdf  output_%d.pdf 

and aftewards I join them all via command:

pdfunite $(ls -v output_*.pdf | tr '\n' ' ') out$(date  +%Y-%m-%d_%H_%M_%S ).pdf

This joins:

output_1.pdf output_2.pdf output_156.pdf output_157.pdf  

into:

out2014-12-14_23_25_36.pdf

May be there is an easier way how to cope... :-)

Installation instructions:

sudo apt install poppler-utils

You can also use jPDFTweak, pdfsam or pdfjam.

(That said, I use pdftk.)