PDFtk Server is a simple commandline tool for doing everyday things with PDF documents. You can use it to merge PDF documents or collate PDF page scans, split PDF pages into a new document, rotate PDF documents or pages, decrypt input as necessary (password required), encrypt output as desired, fill PDF forms with X/FDF data and/or flatten forms, generate FDF data stencils from PDF forms, apply a background watermark or a foreground stamp, report PDF metrics, bookmarks, and metadata, add/update PDF bookmarks or metadata, attach files to PDF pages or the PDF document, unpack PDF attachments, burst a PDF document into single pages, uncompress and re-compress page streams, and repair corrupted PDF files (where possible).
CPDFTK is a commercial, supported implementation of pdftk. It is a set of command line tools for manipulating PDF files with the same interface as the popular open source pdftk tools. It can split, merge, linearize, scale, rotate, crop, encrypt, decrypt, watermark, bookmark, annotate, attach, and impose files.