Do you need a lot of features in the software that you use to combine your PDFs? Then look no further than pdfmeld. pdfmeld is one of the most powerful and flexible piece of PDF software for Linux.
To use pdfmeld you type something like this at the command line:
pdfmeld has literally dozens of options. These options include adding bookmarks to a PDF, encrypting the PDF file, and adding information like title, author name, and subject. For a full list of the options, check out the documentation. While it sounds complex and difficult to use, pdfmeld really isn't. You'll quickly find that you'll only regularly use a handful of the options, and can forget about the rest.
pdfmeld doesn't just combine PDF files. You can use it extract pages from a PDF, rearrange the pages in a file, rotate pages, and even touch up text. In fact, pdfmeld packs many of the features of Adobe Acrobat -- all in a package that weighs in at just over 1 MB.
pdfmeld's range of options are its greatest strength. Like joinPDF, pdfmeld automatically compresses the resulting PDF. It's also very fast: it only took a few seconds to join three 20 page PDFs.
There is very little that I found wrong with pdfmeld. One problem that I did encounter, that I didn't see with Ghostscript or joinPDF, was the error message "Page Contents Object has Wrong Type" when I tried to open a merged PDF in Acrobat Reader. This happens when an empty page contains contents information. This only happened twice, when I added a cover followed by a blank page to a particular document. It was annoying, but luckily this wasn't a common error. On top of that, pdfmeld isn't free software. Linux purists may balk at paying for the software, but not everyone will.