I use pdftk mainly. But here are some others to consider:
pdfsam (PDF Split and Merge): "pdfsam is an open source tool (GPL license) designed to handle pdf files"
PDFJam "A small collection of shell scripts which provide a simple interface to much of the functionality of the excellent pdfpages PDF file package (by Andreas Matthias) for pdfLaTeX." (You can also use pdfLaTeX directly.)
jPDFTweak: "jPDF Tweak is a Java Swing application that can combine, split, rotate, reorder, watermark, encrypt, sign, and otherwise tweak PDF files."
Inkscape: is a vector graphics editor that can both import PDF pages into its native SVG format, and also export as PDF.
Calibre: Open source ebook management software that can convert PDFs to other formats, and manipulate them in other ways. Comes with command line tools such as pdfmanipulate which can be useful.
Ghostscript of course can do a lot of things with PDF files too.