Introduction

I used WinEdt, MikTex, and pdflatex on WindowsXP to prepare my thesis. As such, some system specific tweaks were required. The problems along with the fixes I used are listed below.

Details

Long chapter titles do not wrap to multiple lines in the Table of Contents

This is caused by the default options passed to the hyperfer package in the example.tex file. Changing the first option from ps2pdf to pdftex and chaning the breaklinks option from false to true will correct the problem. (Note: Chris has indicated that there are compelling reasons not to use pdflatex. I don't know the reasons, but I'm sure he can give you more information if you're interested.)

With these changes, my \usepackage command for the hyperref package looks like this:

\usepackage[
    pdftex,
    bookmarks=true,
    breaklinks=true,
    raiselinks=true,
    pdfborder={0 0 0},
    colorlinks=false,
    ]{hyperref}

References section does not appear in the Table of Contents

Chris's hack in the example file does work with my configuration. However, before he came up with that one, I used another solution which I will post here for completeness.

The tocbibind package allows users to control which sections are included in the Table of Contents. This pacakge is included in the default MikTek installation. The commands to use it are shown below.

\usepackage[nottoc,notlof,notlot]{tocbibind}
\settocbibname{References}