In a terminal type:
sudo apt-get install pdftk
Now you can merge pdf files by putting them in the same directory and in a terminal typing:
pdftk 1.pdf 2.pdf 3.pdf cat output merged.pdf- substituting the number for the names of the pdfs files.
More options can be found on the pdftk website. pdftk can split files, encrypt, decrypt, password protect, rotate an image, etc.