In reply to foxjerk:
would second suggestions to use referencing software - it saves hours of work and stress.
I'm currently writing up my phd, and have run a paperless office for my MSc and PhD. I use a Mac.
Used Papers app for a while, but prefer Sente - which I see noone else has mentioned.
Sente is very good:
- it populates the reference metadata file fairly automatically
- deals well with managing large numbers of PDFs (including books and journal articles)
- can annotate & highlight any OCR'd PDF
- has iPad app so I can work while travelling. not had any problems with creating annotated bibliographies or reference lists for papers/ thesis
- it reformats reference lists quickly if you need to for different journals etc