Note: I've recently launched Toolbelt, a tool that also allows merging PDFs online without having to download anything. No size limit and super quick!
This commandline-tool allows you to quickly merge multiple PDF files into one.
It searches the current work directory and all subdirectories recursively for PDF files and lists them to you. You can then select and deselect files that you want and rearrange them.
After that, you can specify the outputname and PDFJoin does the rest for you.
To get started, you need NodeJS and Java v6+ installed.
You can call the app in the directory in which you want to search for PDF files directly with
$ npx pdfjoin
without installing anything, or you can install it globally and invoke it from there:
$ npm i -g pdfjoin $ pdfjoin