When writing large documents, eg. greater >100 pages, I prefer to use Latex, Bibtex, Subversion, and Kile.
Latex is brilliant for large documents. As it says, it lets you separate content from how its displayed. It produces beutiful results, especially for technical documents with maths etc. With the addition of PSfrag you can even put Latex formatting into your eps graphs and diagrams.
Bibtex is still my preferred reference manager. Most journal have style files for their preferred bibliography.
When I started using subversion with my documents it was great. With a networked subversion server I could get the latest version of my document anywhere. You could track changes, and see when you last worked on a section.Being able to find out what you changed in a particular chapter last month is handy. I now have a subversion repository that I has sub-directories for all my latex documents. I started using subversion while writing up my PhD and have used it to keep track of all my latex documents since. If your unfamiliar with subversion then kdesvn is a great GUI tool that integrates into KDE file management.
Kile is a good kde frontend to latex. I used emacs for 10+ years and loved it, but Kile's integration with the KDE desktop and its specialisation for latex make it a good choice of editor. Of course can use any text editor you want with latex, but choosing one designed for latex mark up and lots of shortcuts makes life easier.
WYSWYG editors like OOO and MSO are really only good for short documents. I've had to deal with these programs for documents >50 pages and they really become a pain.
Elivs