In the paradigm of service oriented science, scientific computing applications and data are all wrapped as web accessible services. Scientific workflows further integrate these services to answer complex research questions. However, our earlier study conducted on myExperiment has revealed that although the sharing of service-based capabilities opens a gateway to resource reuse, in practice, the degree of reuse is very low. This finding has motivated us to propose ServiceMap to provide navigation facility through the network of services to facilitate the design and development of scientific workflows. This paper proposes ReputationNet as an enhancement of ServiceMap, to incorporate the often-ignored reputation aspects of services/workflows and their publishers, in order to offer better service and workflow recommendations. We have developed a novel model to reflect the reputation of e-Science services/workflows, and developed heuristic algorithms to provide service recommendations based on reputations. Experiments on myExperiment have illustrated a strong positive correlation (with Pearson correlation coefficient 0.82) between the reputation scores computed and the actual performance (i.e. usage frequency) of the services/workflows, which demonstrates the effectiveness of our approach.