This is a Java solution. If you want to create PDFs in PHP, FPDF ( http://www.fpdf.org/ ) works great and has tons of addons. The library FPDI ( http://www.setasign.de/products/pdf-php-solutions/fpdi/ ) uses FPDF and is probably the closest thing to PDFBox in PHP when it comes to working with existing PDFs.
A few years ago I wrote a library using FPDF + FPDI that can overlay barcodes on existing PDFs: http://chir.ag/projects/pdfb/ and it has proven to be a very stable and capable setup. We use this at my work to generate over 10,000 pages of PDFs daily from a tiny Apache server.
(PDF tools, pdftk 2006, toolkit is win/linux cli)
http://www.pdfhacks.com/pdftk/
http://www.softpedia.com/get/Office-tools/PDF/GUIPDFTK.shtml
(using PyPDF)
http://pieceofpy.com/index.php/2009/03/05/concatenating-pdf-...
(2 from softpedia, freeware - Junko OK, 1.3 MB zip)
http://www.softpedia.com/get/Office-tools/PDF/silkodyssey-PD...
http://www.softpedia.com/get/Office-tools/PDF/Junko.shtml
(uses C# free lib http://itextsharp.sourceforge.net/)
(Mac: PDFLab at:)
http://www.iconus.ch/fabien/