Link quality estimation (LQE) in wireless sensor networks (WSNs) is a fundamental building block for an efficient and cross-layer design of higher layer network protocols. Several link quality estimators have been reported in the literature; however, none has been thoroughly evaluated. There is thus a need for a comparative study of these estimators as well as the assessment of their impact on higher layer protocols. In this paper, we perform an extensive comparative simulation study of some well-known link quality estimators using TOSSIM. We first analyze the statistical properties of the link quality estimators independently of higher-layer protocols, then we investigate their impact on the Collection Tree Routing Protocol (CTP). This work is a fundamental step to understand the statistical behavior of LQE techniques, helping system designers choose the most appropriate for their network protocol architectures.