In this paper we explore the possibility of using Web links to study collaborations between organisations, combining the results of qualitative analysis of interviews and quantitative analysis of linking patterns. We use case studies of scientific intermediaries, that is, organisations that mediate between the science system and other social actors (the market, the government etc) and argue that it is becoming increasingly important for such intermediaries to use the Web to indicate their strategic alliances. We analyse links between these organisations, together with primary sources such as organisational charts and internal reports, and find that these organisations indeed use outlinks to point to their collaborators and more specifically outlinks from specific depths. This supports our argument that links can be used to study the developments in science and the environment of scientific intermediaries. We discuss these findings in terms of their relevance for science studies and webometrics.