MacOS – Convert .help to .pdf

Unfortunately Apple's PDF export doesn't create the standard PDF Table of Contents, you'll need to use other software to add one to your existing PDF.

There are a variety of options at a variety of prices:

OpenOffice Writer: A hassle, but it's the only free option I've seen. You'd export your Pages file as Word or rtf and then open it in OpenOffice Writer and then export to PDF; it will generate a PDF table of contents as part of the export.

PDF Outliner: Just $4.99 in the Mac App Store, it's probably the best combination of cheap and easy. It's specifically designed to add a PDF Table of Contents to your document.

PDFpenPro: At $99.95 it's not cheap but it does pretty much everything the full version of Adobe Acrobat does and is much, much cheaper.

Acrobat X Standard: The real thing from Adobe for "just" $449.95. If you only need to do this now and you'll be done creating PDF Tables of Contents within 30 days you can download the free trial. After 30 days, though, you're out of luck.

For the command-line I can recommend:

pdftk, the PDF Toolkit (for the Snow-Leopard installer you can try Pacifist to get the binaries or use the older version)

Merge PDF Documents

Split PDF Pages into a New Document

Rotate PDF Pages or Documents

…

If your PDF is edit-protected, you may want to try qpdf (via e.g. homebrew) to remove the restrictions first.

QPDF is a command-line program that does structural, content-preserving transformations on PDF files. It could have been called something like pdf-to-pdf. It also provides many useful capabilities to developers of PDF-producing software or for people who just want to look at the innards of a PDF file to learn more about how they work.