The book was written using the free OpenOffice software word processor Writer and I strongly recommend it. As far as I can see the functionality is no worse than Microsoft Word and it seems at least as reliable. The Writer index function was used to create the index of the book.
I used the spreadsheet software Calc from the same suite to collect my references - which numbered around 1500. The function to have a hyperlink in cells meant that I could link directly to any digital copies of papers I had stored on disc and to any useful webpages I found.
Inserting the references in numbered order into the document was the trickiest and most time-consuming part and for that I used some Basic software I developed myself.
Since finishing the book I have discovered the add-in for Mozilla Firefox called Zotero. This allows you to collect references, make links to copies and insert citations (in many formats) into OpenOffice text as you go along. I am now managing 2000 references for a new project and it seems to work very well. It is, by the way, free.
The other elements of the OpenOffice suite seem to work well too. Impress is an equivalent to Powerpoint and Base to Access.
The system is sponsored by Sun Microsystems and plenty of information and downloads can be found at the OpenOffice website.