The Journal of the American Society for Information Science and Technology offers a great comparison of different tools for mapping science in their July 2011 issue. These tools are great for leveraging bibliographic data to understand research efforts over time, collaboration, citation patterns, and much more. I wish I had seen this paper when it was published in July!
Cobo, M., López-Herrera, A., Herrera-Viedma, E. and Herrera, F. (2011), Science mapping software tools: Review, analysis, and cooperative study among tools. Journal of the American Society for Information Science and Technology, 62: 1382–1402. doi: 10.1002/asi.21525
I’m partial to the Network Workbench Tool and Sci2 Tool and have used them for various purposes. Both were developed by the Cyberinfrastructure for Network Science Center at Indiana University. Both tools are freely available, both are able to utilize data from diverse sources, and both offer great support materials and tutorials to get you up and running quickly.