In reply to David Barratt:
I would second what you said about doing it as you go along. If you've got to this stage, with all the papers, and haven't put the details into any referencing software it might actually be quicker to just do it manually. That's what I ended up doing for my PhD thesis. It was a slog, but as long as you do it carefully and logically its not to bad. Your dissertation can't be anywhere near as long as my thesis was! (note, if I did it again I would have used referencing software from the start without a doubt, to plan to do it manually would be insane, but hindsight is wonderful and some seemingly obvious things aren't!)