My mother is working on her Ph.D. and has asked me to work with her on setting up a research suite of tools for managing bibliographies, related research, paper and article authoring. It will also likely be used to manage and produce her Ph.D. dissertation if we are succesfull.
It has been about 14 years since I completed my degree and the academic world has changed substantially. Whereas I spent a lot of time in the periodical stacks and the various journal indexes, all that is now done online ... without ever darkening the door of the library.
This shifts the tools emphasis away from 3 x 5 cards for bibliographic information to tools that automatically download the data from the online library and even produce bibliographies, integrate into Microsoft Word.
Some examples of tools are Reference Manager, End Note and Pro Cite which are all from Thomson ISI Researchsoft. These tools are all mature and widely supported by online research databases. The trouble is that your research is then locked up in their proprietary databases or online services.
I am exploring a different option. The standard bibliographic data format in the sciences is bibtex and the standard environment for authoring and publishing seems to be Latex based on Don Knuths Tex for typesetting. These two standard tool sets are tightly integrated. So my first run at this is to setup the following tools as an integrated research and authoring suite:
Miktex for Latex/Tex support on Windows
Lyx for Latex authoring environment
BibDB for Windows as the bibtex bibliography database manager.
It would be nice to hear from anyone who is currently using such a setup for writing and research management.