GUI and command-line tools to split and merge PDF documents, rotate and rearrange pages; supports encrypting/decrypting of PDF documents, setting permissions, adding front or back cover, extracting attachments, filling the metadata
Open-source C library in development; when done, will provide functions to implement all features of PDF 1.7 specification. (Due to the availability of Poppler, as of 6 October 2011, GNU PDF is no longer considered a "high priority project" by FSF.)
Okular: Supports a range of annotation types. Annotations are stored separately from the unmodified PDF file, or (since version 0.15 with Poppler 0.20) can be saved in the document as standard PDF annotations.
Xournal: Allows for complex and customizable annotations by freehand drawing, a shape recognition tool, multiple colours and text fonts. In addition, there is a rule tool for straight lines, highlighting and underlining. Annotations may be copied, pasted and easily moved. Annotations may also be in complex scripts such as Tibetan through SCIM input. Annotations are stored separately from the unmodified PDF file, but the annotated document can be exported to PDF.
Evince: Supports addition and removal (since version 3.14 ), of basic text note annotations.
Preview: Mac OS X's default PDF viewer (in Mac OS X v10.5 and later, it also can rotate, reorder, annotate, insert, and delete pages. It can also merge files, create new files from existing files, and move pages between files.)
Adobe Acrobat: Can convert files into PDF or convert PDF files into other formats
ABBYY FineReader: Commercial PDF converter which converts PDF into Word (.doc), Excel (.xls), PowerPoint (ppt), and more
deskUNPDF: PDF converter to convert PDFs to Word (.doc, docx), Excel (.xls), (.csv), (.txt), more
GSview: File:Convert menu item converts any sequence of PDF pages to a sequence of images in many formats from bit to tiffpack with resolutions from 72 to 204 × 98 (open source software)
gDoc Fusion: Proprietary, shareware; PDF views, edits, converts documents into PDF, XPS or Microsoft Word document; after 30 days a watermark is placed on documents in shareware version
OmniPage: Converts to and from PDF and other formats with many options.
PDF-XChange: PDF Tools and PDF-XChange print driver allow conversion from many formats to PDF. A "lite" version of the print driver is free for non-commercial (home and academic) but places a watermark on documents
Qiqqa: Converts Microsoft Word document and Web Pages to PDF.
SaveasPDFandXPS: Freeware add-in for Microsoft Office 2007; converts documents in standard Microsoft Office formats, e.g. Word, Excel, Powerpoint, into PDF format.
SWFTools: 'pdf2swf component converts PDF to SWF – command line with GUI wrapper
Freeware reader; commercial full version available
As with Adobe Acrobat, Nitro PDF Pro's reader is free; but unlike Adobe's free reader, Nitro's free reader allows PDF creation (via a virtual printer driver, or by specifying a filename in the reader's interface, or by drag-'n-drop of a file to Nitro PDF Reader's Windows desktop icon); Ghostscript not needed.
PDF Tools allows creation of PDFs from many types of source input (images, scans, etc.). The PDF-XChange print driver allows printing directly to a PDF. A "lite" version of the print driver is free for non-commercial (home and academic) use.
gDoc Fusion: proprietary/shareware desktop product to create, review, edit, share or archive PDF and XPS documents. After 30 days a watermark is placed on documents in shareware version.
IceCream Split & Merge: It offers multiple array modes that enables users to split and merge Portable Document Format (PDF) documents, including password protected and encrypted files.
LibreOffice: free (MPLv2) GUI tools to manipulate, split, merge, encrypt and decrypt PDF files
Nitro PDF Pro: a proprietary commercial PDF creator/editor with an interface styled after Microsoft Office; replicates most or all features of the Adobe Acrobat full commercial version; offers a separate freeware reader (which also supports PDF creation, annotation, collaboration and signing); Ghostscript not additionally needed.
PDF Studio: Proprietary software for viewing and editing PDF documents
pdftk: free (GPL) command-line tools to manipulate, edit and convert documents; supports filling of PDF forms with FDF/XFDF data
PDFSaM: free (GPLv2) command-line and GUI tools to manipulate, split, merge, encrypt and decrypt PDF files
PDF-XChange Viewer: Freeware PDF reader, tagger, editor (simple editions) and converter (free for non commercial uses).
Solid PDF Tools: Convert PDFs into editable documents and create PDFs from a variety of file sources.
Microsoft Word 2013: Proprietary desktop software. The 2013 edition of Office allows editing PDF files.
Adobe Reader: Adobe's PDF reader is free only for personal use. For commercial use, Adobe Reader should be purchased. For instance, if your software uses Adobe Reader for things like printing, you and your customer will have to purchase Adobe Reader if it qualifies as a commercial product 
Evince: a free (GPL), open source PDF reader. Part of the GNOME desktop environment. Windows port available since version 2.28.
Foxit Reader: Proprietary/freeware PDF reader, supports FDF import/export, saving filled forms; other extended functionality available via purchasable plugins.
gDoc Fusion: Proprietary/shareware to view PDF, XPS, Microsoft Word document, Microsoft Excel spreadsheet, Microsoft PowerPoint presentation or image files, included in the evaluation version of the product. Shareware version places a watermark on documents after 30 day eval.
Javelin PDF Reader: A full functionality PDF reader with support for DRM using encoded and encrypted PDF files in Drumlin's DRMX and DRMZ formats.
Nitro PDF Reader: Freeware (though proprietary) PDF reader and creator. Supports three methods (specifying the file within the reader's interface, or dragging-'n-dropping a file onto the reader's Windows desktop icon, or "printing" to a virtual printer driver) of PDF creation (Ghostscript not additionally needed), saving filled forms (AcroForms), text typewriter, markup/collaboration, and stamp signature (document signing).
Nuance PDF Reader: Freeware (adware) PDF reader, supports saving filled forms, partial support for XFA forms; enables the capability to convert PDF files to MS Word or Excel files through Nuance website.
PDF-XChange Viewer: Freeware viewer with free OCR, supports FDF/XFDF import/export, saving filled forms, extended markup and export to image capabilities.
Qiqqa: Freeware PDF reader, indexer, tagger and annotator. Supports OCR and export of PDF text and images.
Sumatra PDF: A free (GPL), open source PDF reader. It also supports DjVu, XPS, CHM, Comic Book (CBZ and CBR) and eBook (EPUB & MOBI) file formats. Supports automatic reloading of PDF files.
STDU Viewer: A freeware for non-commercial usage PDF reader. It also supports DjVu, Comic Book Archive (CBR or CBZ), XPS, TIFF, TXT and image file formats.