PDFCombo is an app to combine multiple PDF files. Unlike other apps, PDFCombo preserves the Table of Contents (TOC) in the combined PDF. It can also add a new top-level TOC entry for each contributing PDF. This can be useful to keep a complex TOC neat & tidy, or to add a TOC item to demarcate contributing PDFs.
For example, if you've created PDFs using the File > Print... dialog in Mac OS X or you've got several scanned PDFs, you can combine them into one PDF with PDFCombo with automatic TOC entries to mark the first page of each contributing PDF.
PDFCombo is a free app available on the Mac App Store.
For editing the TOC in any PDF, consider PDFOutliner.
See also notes to PDFCombo 1.0.2 (published 04/21/2014) and PDFCombo 1.0.3 (published 05/15/2014.)
[2017 Update]: PDFSpeech is a new powerful app that can combine multiple PDF files into a PDF Pack. See this short walkthrough on how to print an entire book from safaribooksonline.com to PDFSpeech to create a PDF with a table of contents. PDFSpeech also includes the ability to insert clipboard contents as PDF into the Pack, and multiple pages selected & copied from Preview. The primary use of PDFSpeech is to help you read more by tapping into text-to-speech technology, and it enables easy control over pronunciations so you can listen to the generated speech for extended periods without any glaring mistakes.