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).
jPDFProcess is a Java library to work with PDF documents which can be used to deliver customized PDF content to your users or to process and manipulate incoming PDF content. The library has a simple interface to work with PDF documents and is designed to be integrated easily and seamlessly into your PDF document workflow. jPDFProcess provides the functionality found in many other Qoppa Software libraries, including printing, setting permissions and security, creating and assembling documents, digital signing, working with form fields, extracting text, and more. It can work with PDF documents from files, URLs, and input streams, and can save documents to files and output streams, so it can serve documents from a J2EE application directly to a client browser without any temporary files. jPDFProcess is platform-independent, and can be used in any environment which supports Java.
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.