Link analysis in various forms is now an established technique in many different subjects, reflecting the perceived importance of links and of the Web. A critical but very difficult issue is how to interpret the results of social science link analyses. It is argued that the dynamic nature of the Web, its lack of quality control, and the online proliferation of copying and imitation mean that methodologies operating within a highly positivist, quantitative framework are ineffective. Conversely, the sheer variety of the Web makes application of qualitative methodologies and pure reason very problematic to large-scale studies. Methodology triangulation is consequently advocated, in combination with a warning that the Web is incapable of giving definitive answers to large-scale link analysis research questions concerning social factors underlying link creation. Finally, it is claimed that although theoretical frameworks are appropriate for guiding research, a Theory of Link Analysis is not possible.