PDFtk - PDFtk is a simple tool for doing everyday things with PDF documents.
PDFsam - PDFsam Basic, a free, open source, multi-platform software designed to split, merge, extract pages, mix and rotate PDF files
AutoMetadata - AutoMetadata is a tool for exploring and manipulating metadata, document properties, and viewer preferences in multiple PDF documents.
PDF-Shuffler - PDF-Shuffler is a small python-gtk application, which helps the user to merge or split pdf...
Edit PDF metadata - Edit PDF metadata is an online tool from PDFCandy that can manipulate PDF info and metadata.
Stapler - Manipulate PDF documents from the command line