Based on discussion in the mailing list: http://groups.google.com/group/rhodecode/t/f341f5db819890e0
Instead of organising repositories solely by using repository groups it would be nice to be able to specify multiple user defined tags for a single repository (e.g. "tools", "python", "web", "ui"). These tags can then be used when searching for repositories.
Furthermore breadcrumb navigation (http://www.smashingmagazine.com/2009/03/17/breadcrumbs-in-web-design-examples-and-best-practices-2/) could be used to create filters for the displayed repositories.