When doing a PhD, next to writing, the most important thing you do is probably reading. It is necessary to read what others have done to find interesting research questions and to avoid doing the same as other researchers. It is at the same time important to position your own work in relation to what others have done by referring to their work when you write.
It is imperative to manage the publications your read and the bibliography information for these publications. Searching for something you know you have read somewhere and identifying missing references is really a pain. It is therefore very wise to managing your bibliography using for instance BibTeX, Endnote or similar tools.
As a Latex person I will focus on the tool I use for managing bibliographic information (BibTeX), pdf files, notes and categorization of all this information, Aigaion. Other tools worth checking out are CiteULike and Zotero. I have used CiteULike (a web service) a bit but the lack of quality BibTeX information made med abandon it “long” time ago. Recently I have started using Zotero (a in-browser tool) a bit but primarily for gathering data (it does a very good job). Other people who use it recommends it warmly. However, my recommendation is to share you bibliograhpy with your friends and colleagues using an internet based tool called Aigaion.
I will try to explain why I stared using Aigaion. First, since I am using several computers and both Windows and Linux I wanted a system which was portable. Aigaion allows me to easily export all the information from the system as BibTeX or RIS files. These files can simply be put into a revision control system. Combining the BiBTeX text files with Subversion works like a charm. Second, I wanted to be able to share the publications and the BibTeX information with my colleagues. Aigaion is a web based system which allows several users to share and manage the same information and the same pdf files, and collaborately improve it. This is probably the main reason why I started using it. It is easy to give a colleague access to a publication or I can easily email a publication to someone using a feature I (proudly) contributed myself.
Moreover, being a web system written in PHP it is easy to extend and integrate it. It has a fairly stright forward MVC architecture and it is built on top of a framework called CodeIgniter. I use Aigaion to list my publications in my web site http://oyvindhauge.net (see publications) and our publications at the department in wiki about open source software research http://www.research.idi.ntnu.no/oss (see publications).
So if you are in need of a system for managing your bibliography or if you just need a system to manage your own publications and print them in your own or your department’s web page you would want to chekc out Aigaion. Head over to http://www.aigaion.nl, download it or at least try the demo. It comes highly recommended!