Best Free PDF Tools

Introduction

A PDF tool comes in handy when you need to deal with PDF files such as to merge or split pages, add a header, footer or watermark, highlight or annotate PDF documents, or convert from other files to PDFs or vice versa. In this review, multipurpose programs offering general features for merging PDF files, splitting or re-ordering pages, etc 
General Tools - Merge, Split, Reorder & More

PDFill PDF Tools
PDFill PDF Tools is my favorite with its nice, clean user interface covering most  functions, including merge pdf files, split or reorder pages, rotate or crop pdf pages, add headers and footers complete with page numbers, etc.

Watermarks can be added either by typing in some text (such as ‘DRAFT’ for documents to be reviewed), or by inserting a background image in PDF format.
Some additional features are supported, such as encrypt and decrypt with security options; reformat multiple pages into one page; delete, flatten or list PDF form fields; convert PDF to images or vice versa; and convert a PostScript file to PDF.
Note that PDFill PDF Tools comes bundled with PDFill PDF Editor, which is not free. However, you can run PDFill PDF Tools separately after installation. The free software part of the package does not support functions such as converting PDF to text, making annotations, etc. But those features are all available in the Specific Tools listed in the next section. 
PDF Shaper
Another free application PDF Shaper offers a different set of PDF tools which include Split and Merge PDFs, Encrypt and Decrypt PDF, Convert PDF to Image and vice versa, Extract Images from PDF, Rotate Pages or Sign PDF, Extract Text from PDF and Convert PDF to Word RTF.

PDF Shaper lacks such tools such as adding watermark, adding header and footer, reorder pages, crop pages, adding PDF information, etc. available in PDFill PDF Tools, but it has some other tools that PDFill PDF Tools does not have, such as Extract Text from PDF and Convert PDF to Word RTF.
PDF Shaper sports a clean user interface and it's easy to use. However, the function of Convert PDF to Word RTF only did up to three pages of conversion and specifying pages for splitting PDFs encountered an error when tried.
During installation of PDF Shaper, uncheck the option for bundling a toolbar or any other component which you do not need. 
PDFTK Builder
PDFTK Builder is a useful alternative. The big advantage of PDFTK Builder is that it can merge or reorder selected pages of PDF files at one go, which is much simpler if you have a lot to do.

PDFTK Builder also supports split, rotate, background/stamp and encrypt features. Besides these, it has no other additional features.
It's worth noting that PDFTK Builder lacks a basic function (available in PDFill PDF Tools) for watermarking PDF documents with background text—this can be important if you need to mark your documents as 'Confidential', 'Draft', etc.

jPDF Tweak
If your priority is to get the maximum number of features from a single freeware package, then jPDF Tweak will be a good choice. However, its user interface is not as straightforward as in either of the two applications reviewed above. Its merge, split and reorder functions are available under the ‘input’ tab, and a new filename has to be entered in the ‘output’ tab.

This feature rich program allows you to rotate, watermark and format multiple pages. You can change page numbers and chapter bookmarks. And jPDF Tweak also offers encryption functions and lets you add attachments to PDF documents.
Additionally, jPDF Tweak enables you to set viewer preferences and document properties, including title, author, subject and keywords. 
PDFsam
PDFsam (PDF Split and Merge) is well worth trying if you need to visually re-order or recompose multiple pages of PDF files.

You can mix, merge or extract, split and rotate pages by specifying the page numbers. However, PDFsam also lets you re-organize PDF pages in a thumbnail view. In this mode, you can easily work with thumbnails to merge, delete, rotate or re-order PDF pages and save the results as another PDF file.
Since PDFsam is a Java application, it will run on any operating system that supports Java. The basic version of PDFsam is free for use. The installer is bundled with an advertising program OpenCandy but you can get from here a standalone zip file with no such bundle. 
PDF Shuffler

After importing one or more pdf files to PDF Shuffler, the various pages appear as thumbnails, making it easy to merge, re-order or delete. You can right-click a thumbnail to rotate or crop a page before exporting to a new pdf file.
PDFShuffler is a small application running on Linux. Some distros, such as Ubuntu, include PDF Shuffler in the repository for ease of download and setup. 

Specific Tools

Edit a PDF File
Oracle PDF Import Extension (formerly Sun PDF Import Extension) allows you create a hybrid pdf file with LibreOffice or OpenOffice Writer. A hybrid pdf file is basically a pdf file containing an embedded odf source file. The beauty of this type of file is that not only can it be viewed with a normal PDF viewer, it can also be opened for full text editing with LibreOffice or OpenOffice Writer in 100% layout accuracy. See this article A PDF File Allows Editing in 100% Layout Accuracy for details.
If you need to edit a normal or non-hybrid pdf file, LibreOffice or OpenOffice Draw is one of the free options available. You can use it to edit small portions of text, add or remove images and so on with no layout adjustments.
Convert PDF to Text
FreeOCR.net
Some PDF to TXT Converter is a light tool which preserves text and layout while supporting drag and drop, batch conversion and encrypted pdf files. Alternatively, try the latest version of Nitro PDF Reader which gives you an option either to keep text in paragraphs for easy re-alignment, or to break each line to a width of any number of characters of your choice.

FreeOCR.net is a good scan and OCR (Optical Character Recognition) program which lets you extract text from scanned PDF documents. Moreover, images from scanned PDF documents can be selected and placed on the clipboard. For an online OCR solution, try Free-OCR.com.
Convert PDF to Word/Excel
Free online conversion is available from Nitro PDF for PDF-to-Word Converter and PDF-to-Excel Converter. Choose the file you need, click the "Convert" button and check your inbox for the converted files.
Convert Various Formats to PDF
7-PDF Maker

If you are using office applications such as LibreOffice or OpenOffice, or word processors such as Jarte, they come with a feature to export files to PDF. Newer versions of Microsoft Office also allow a free add-in for saving documents as PDF.
Whether you choose to use 7-PDF Maker or any of these applications, you should find that clickable hyperlinks and bookmarks are nicely conserved in the converted or exported PDF files, along with the original page layouts.
An alternative approach is to install a virtual PDF printer, such as Bullzip, which will 'print' out PDF files of text or other contents. Note, however, that clickable hyperlinks and bookmarks will not usually be preserved in the resulting PDF file.
i2pdf
If you only need to convert image files to PDF, my favorite would be i2pdf. It works even better than the tool "Convert Images to PDF" included in PDFill PDF Tools. Download and unzip i2pdf and run the executable directly (no installation required). This program is portable and user friendly—just drag and drop the images on the program window, click the "Build PDF" button and it's done. When setting the page output, "paperless" format is a helpful option if you'd like to convert portrait or landscape images to the PDF file and view them on the screen without blank paper margins.

How about converting files to PDF online? 7-PDF Web Portal and many other websites such as kool Converteror Document Converter eXPress also offer online conversion to PDF.
Extract Images from PDF
Some PDF Images Extract is a good choice. You can extract all images from several PDF files by batch or pull images from selected pages in a PDF file. Images can be saved in jpg, bmp, png, tiff, gif or tga formats. It costs no money to use this application, but it is nagware which prompts a dialogue to ask for registration with payment each time you use it.
Annotate PDF Documents
PDF-XChange Viewer enables you to annotate PDF documents. It allows a variety of operations, including highlighting, crossing or underlining text; drawing shapes; stamping and filling out PDF forms with a built-in typewriter; insert, edit or rename bookmarks. Unfortunately some advanced features are available only to the paid-for Pro version.
The good news is that now Foxit Reader has made this particular feature, together with most other basic annotating tools, available for free. If you're looking for an alternative, Foxit Reader is definitely a good choice.
For Linux users, Okular is a good try. It supports annotations, highlighting, drawing lines and shapes, adding textboxes and stamps, and selecting and saving part of a document as text or in an image format.
Create and Edit Bookmarks
JPdfBookmarks
JPdfBookmarks allows you to create and edit bookmarks on existing PDF files. You can add bookmarks to quick jump to a certain page of PDF documents, point to another PDF file in the file-system or go a website in a browser.

Bookmarks can be easily renamed or edited. To set a bookmark to jump to a certain paragraph in a page—first browse to that paragraph, then right-click a bookmark, select "Set Destination" then "Replace Current". When completed, save the file as a new PDF file and it's all set.
Make Fillable PDF Forms
PDFescape is a helpful web application which lets you create or fill in PDF forms online, straight from your browser, In addition to creating and editing fillable forms, you can also add text, links and sticky notes, draw basic shapes, and whiteout contents. PDF Escape is now entirely free. If you want to save your work and return later you'll need to register.
Crop PDF Pages
Briss is a cross-platform Java application which makes visual cropping of PDF pages much faster and easier. You just load a pdf file, draw one or more rectangles with a mouse to crop the regions you want from a page and then save them as another file. If you load a PDF file with multiple pages, you can see the odd and even numbered pages overlaid and crop them easily in one go.
Set Viewer Preferences and Metadata
BeCyPDFMetaEdit is a good find. It allows you to edit most metadata such as title, subject and author of your PDF files, and customize viewer preferences, slide show page transitions, page labels, etc. Other than the GUI version, it also has a command version for batch processing with parameters explained in the help file supporting most of the application functionality.
"Tweak PDF" is another choice with a simple user interface, but it lacks a slideshow setting and some other features. The program is portable and available for download at Portable Freeware. It has been scanned cleanon VirusTotal. (NB: The link to the developer's homepage is not provided here as it has a bad WOT rating upon checking).
Digitally Sign a PDF File
DigiSigner

The latest version of this application allows you to create a certificate or PFX file with DigiSigner proper. Additional features include the ability to create and edit multiple signature appearances using fonts and images, batch signing, add text and images to documents, etc.
Compare Two PDF Files
DiffPDF is a portable open-source application for you to compare two PDF files and see their differences in words, characters or appearance. To compare PDF files, select two different PDF documents via the File #1 and File #2 buttons then click Compare. You can also save your comparison result as a PDF file. The program runs on multi platforms including Windows, Linux and Mac OS X.
Recover Forgotten Password
Try PDFCrak which runs on Linux or DOS (the version for DOS is available for download here). The only supported usage of this software is to recover passwords and/or content that you own but have lost access to as stated in the FAQ.
Booklet Printing
Gimposition (or Govert's Simple Imposition Tool) allows you to re-order and reformat pages of your PDF document to prepare for booklet printing with a foldmark, 2-up printing with page separation lines, or place two equal copies side by side with cutmarks on a top page. No installation is required, just unzip the download, run the executable. It's straightforward, fast and easy to use. 
Other Functions
To add attachments to a PDF, try "PDF Bundle" available for download at Softpedia. The program has been scanned clean on VirusTotal. (NB: The link to the developer's homepage is not provided here as it has a bad WOT rating upon checking).
To compress a PDF file, try this portable application Free PDF Compressor (last free version 1.12).
Others
The following free applications offer particular functions, some of which are available in the main reviews. They were brought up in comments here or noted from other sources. I am listing them here with brief descriptions and links to the related sites for ease of reference.
  • PDFedit, a free PDF editor with GUI interface, allows for complete editing of PDF documents and changing raw PDF objects. It's currently a beta and not easy to use for average users.
  • Sheel Khanna's PDFTools allows users to join multiple PDFs, split or re-arrange a PDF, encrypt or decrypt and stamp a pdf. It also includes a tool to convert XML to a PDF file.
  • Gios PDF Splitter And Merger allows merging and splitting of documents with drag and drop features.
  • GUI for PDFTK Another GUI for the multi-platform PDFTK for merging and splitting pdf files, as well as various other  functions.
  • PdfMerge allows merging and splitting of documents with bookmark import.
  • Free PDF to Word Doc Converter  converts pdf to doc.
  • Free PDF to Word Converter converts pdf to doc or rtf.
  • SpeedPDF Stamp adds an image as watermark.
  • SpeedPDF Page Numberer allows adding page numbers with variable formats.
  • Freeware pdf Unlocker allows removal of PDF restrictions on printing, editing and copying text.