I’m writing a final-year paper, much like most finishing undergraduates, and I find the following tools for Mac to be very useful:
BibDesk – a free, open-source bibliography manager which supports importing annotations from .PDF file. Outputs citations in BibTeX format (more on this anon). It permits searching JSTOR and library catalogues from within the application, meaning adding bibliographic records for books and articles requires little or no data entry, where existing records exist. It is even possible to connect to your local university’s catalogue, if they provide this service – that would mean you’d get local shelfmarks in your local reading list, which can be useful if you are offline.
Skim – a souped up, free, PDF reader with support for exporting highlighted text, and integrates with BibDesk. If you are reading a journal article which has been OCRd or typeset using TeX, the process of citing that source is as trivial as highlighting the relevant passage, and pasting it into your thesis. BibDesk manages these notes.
MacTeX – TeX distribution for typesetting dissertation. If you don’t want to use this and prefer Word, think about plugins like BibTex4Word that offer simple integration of references into your document, and can automatically generate bibliographies in the same way
Google Spreadsheets – I use this to manage quotations from non-digital sources. One workbook with a worksheet per source, works well, not forgetting to fastidiously note page numbers.