You may be interested in some Wikipedia pages we started that aim to provide a comprehensive list of computational tools for visualizing biological data. Starting from http://en.wikipedia.org/wiki/Biological_data_visualization you can access lists of tools for different areas, e.g., alignment, phylogeny, molecular graphics. The pages for systems biology and microscopy currently have only very few tools, and for MRI there is currently no ‘list of’ page. So, we encourage everyone to add their favorite tools! This will give visibility to your favorite tools, and will make these Wikipedia pages a more valuable resource for the community.
Actually there is a back-story to these pages: due to space limitations, in the Nature Method special issue we were very restricted in the number of visualization tools we could mention. As a result, the list of tools cited was ultimately a subjective selection. This was a bit frustrating, as we were forced to remove for the tables several tools we liked. Thus the idea came about to create a more comprehensive list of visualization tools in each field. And the Wikipedia ‘list of’ pages seemed like an ideal place.