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ImageMagick: A powerful suite for image manipulation. It can convert images between formats, resize images, apply various effects, and even convert images to and from PDF.
Ghostscript: Primarily used for processing PostScript and PDF files. It can convert, create, and merge PDF files, and it's often used as a backend for other PDF manipulation tools.
LibreOffice/OpenOffice: Both suites have command-line tools for converting documents between various formats, including PDF. They are especially useful for dealing with office document formats like DOCX, ODT, and others.
Calibre: Best known as an e-book management tool, Calibre also includes powerful conversion capabilities for various e-book formats, and can convert between eBook formats and PDF.
TeX/LaTeX: If you're into more technical or academic writing, TeX and LaTeX are typesetting systems that are ideal for creating professionally formatted documents. They can also be used to generate PDF files.
FFmpeg: While primarily a multimedia manipulation tool, FFmpeg can also be used for tasks like converting videos to PDF slideshows or extracting images from videos and saving them in a PDF.
Asciidoctor: A text processor and publishing toolchain for converting AsciiDoc content to various formats, including HTML, DocBook, and PDF.
Inkscape: A vector graphics editor that can import and export PDFs, useful for editing or creating PDF files with a focus on graphics.
Scribus: An open-source desktop publishing (DTP) application, excellent for creating professional-looking documents, and it can export to PDF.
Docutils: A set of tools for converting plaintext documentation into various formats, including HTML, LaTeX, man-pages, and XML.
PDFtk: A simple tool for everyday PDF editing tasks. It allows you to merge, split, encrypt, decrypt, watermark, and compress PDF files.