Microsoft OneNote is a brilliant tool for visual thinkers, with the ability to position notes anywhere on the infinite page. Furthermore, it provides rich organization capabilities with pages arranged in sections and notebooks. And OneNote for Mac seamlessly syncs all your content across Macs and iPads, and is even editable on the web at onenote online.

With today's update to OneNote, it now supports hyperlinks. PDFoo users can now copy from PDF and paste into OneNote to get a working PDFoo URL. Use the layout flexibility in OneNote for Mac to arrange the content in a way that makes sense to you. For example, the screenshot below shows my quick reference guide to best features in Scrivener for Mac. The blue URLs are pdfoo:// URLs and prefix "scrivmanv25" was assigned in PDFoo to the Scrivener 2.5 Letter-sized user manual in PDF format (available from the Scrivener support website).

It's a good idea to run OCR on the scanned PDF BEFORE you start adding a table of contents (TOC) to the PDF. This is because OCR apps usually create a new PDF, and may not know how to preserve the table of contents from the original PDF when writing out the new PDF. Your hard work in creating the TOC would then be wasted. Moreover, PDFs with OCR text allow text to be selected which can be used to build the TOC quickly as described below.

Note that PDFOutliner comes with an automatic TOC feature which parses the fonts used in a PDF - such as larger fonts used for chapter headings - to build a TOC hierarchy. However this "AutoTOC" feature doesn't work on a scanned PDF (which contain no text) or even an OCR PDF (which do not assign different fonts to chapters/body text etc.) In such cases, you have to "walk" through the PDF page by page, and add TOC entries. Here's how:

• In PDFOutliner, right click on the PDF and select "Single Page" view.
• Make the TOC editor active by clicking on it.
• Use CMD + up/down arrows to move to previous or next page.
• To insert a TOC entry, hit CMD enter. To insert a child TOC entry, hit SHFT CMD enter. These commands insert a TOC entry pointing to top of the current page.
• If your scanned PDF has OCR text, then you can select text on page and hit CMD T to insert a TOC entry with that selected text. This TOC entry will point precisely to where the text occurs on page.
• Use Option + up/down/left/right arrow keys to move around selected TOC entries in the TOC hierarchy.

Save your TOC edits to PDF (CMD S) or hit "Preview" button on PDFOutliner toolbar to create a new PDF.

When you want to read and digest the content in a PDF thoroughly, PDFoo provides an efficient way to do so. The PDFoo app makes it possible to create a link to a specific location in the PDF, which allows you to focus on understanding the big picture while the details are just a click away.

Zengobi's Curio app has an amazing "lists" feature which allows you to position several list boxes on an infinite canvas (known as "idea space" in Curio.) If you select such a list box, and hit CMD+V to paste the clipboard contents, it gets automatically appended to the list. This makes it very convenient to use Curio with PDFoo: copy text from PDFoo, select a list box in Curio, and paste the content with a PDFoo URL appended to the text. The figure below shows a Curio idea space used to work through the OmniGraffle 6 user manual, and includes several "see also" links to detailed content in the PDF. In a similar manner, you can efficiently work through any important PDF using idea spaces in Curio and PDFoo copy-paste.

PDFCombo is a free app for Mac OS X 10.6 and later, available from the Downloads page.

Microsoft Word on Mac OS X doesn't support autosave or versions. It does support AppleScript though, so you can have a script run periodically to force a save. While you could save every X minutes, I prefer to schedule the save after I've stopped typing for a few seconds. This way, the save operation doesn't interrupt while I work.

I use a clever utility app, Scenario ($5, Mac App Store) to schedule AppleScripts which should be run whenever the Mac goes idle for 10 seconds. The following AppleScript snippet will save all open Microsoft Word documents, and should be placed in the ~/Library/Scenario folder used by the Scenario app.

I use such scripts to automatically save all open documents in OmniGraffle, OmniOutliner and other document-based apps. If you're familiar with Keyboard Maestro, the powerful automation utility on Mac OS X, you may prefer the approach described on TUAW.com to autosave Microsoft Word documents.