The combination of pdfpages, hyperref, and bookmark allows for a very neat way of adding an outline to an existing pdf file. For example, we can use the following tex file to add a (partial) outline to my diploma thesis.
\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage{pdfpages}
\usepackage[
pdfpagelabels=true,
pdftitle={Optimization of a Controlled Phasegate for Ultracold Calcium Atoms in an Optical Lattice},
pdfauthor={Michael Goerz},
]{hyperref}
\usepackage{bookmark}
\begin{document}
\pagenumbering{arabic}
\setcounter{page}{1}
\includepdf[pages=1-2]{diploma_thesis.pdf}
\pagenumbering{roman}
\setcounter{page}{1}
\includepdf[pages=3-8]{diploma_thesis.pdf}
\pagenumbering{arabic}
\setcounter{page}{1}
\includepdf[pages=9-]{diploma_thesis.pdf}
\bookmark[page=1,level=0]{Title Page}
\bookmark[page=9,level=0]{1 Introduction}
\bookmark[page=17,level=0]{2 Quantum Computation with Calcium Atoms}
\bookmark[page=18,level=1]{2.1 Trapping of Calcium Atoms}
\bookmark[page=20,level=1]{2.2 Internal Degrees of Freedom and Description of a Single Qubit}
\bookmark[page=21,level=1]{2.3 Description of Two Qubits}
\bookmark[page=22,level=2]{2.3.1 Qubit-Qubit Interaction}
\bookmark[page=23,level=2]{2.3.2 Harmonic Approximation of the Trap Potential}
\bookmark[page=24,level=2]{2.3.3 Summary of Two-Qubit Description}
\bookmark[page=26,level=1]{2.4 Asymptotic Description of Two Qubits}
\bookmark[page=27,level=1]{2.5 Quantum Information Processing with Calcium}
\bookmark[page=31,level=0]{3 Numerical Tools}
\bookmark[page=47,level=0]{4 Phasegate Optimization Schemes}
\bookmark[page=65,level=0]{5 Optimization Results for the Controlled Phasegate}
\bookmark[page=87,level=0]{6 Summary and Outlook}
\bookmark[page=93,level=0]{Appendices}
\end{document}
Assuming that the above is stored as thesis_with_bm.tex, simply running
pdflatex thesis_with_bm.tex will create a copy thesis_with_bm.pdf of
diploma_thesis.pdf that contains the defined outline. Also, the title and
author in the pdf meta data are set, and the pages are labeled
correctly. A great way to post-process scanned documents!