Traditional approach of providing network security has been to borrow tools and mechanisms from cryptography. However, the conventional view of security based on cryptography alone is not sufficient for the defending against unique and novel types of misbehavior exhibited by nodes in wireless self-organizing networks such as mobile ad hoc networks and wireless sensor networks. Reputation-based frameworks, where nodes maintain reputation of other nodes and use it to evaluate their trustworthiness, are deployed to provide scalable, diverse and a generalized approach for countering different types of misbehavior resulting form malicious and selfish nodes in these networks. In this chapter, we present a comprehensive discussion on reputation and trust-based systems for wireless self-organizing networks. Different classes of reputation system are described along with their unique characteristics and working principles. A number of currently used reputation systems are critically reviewed and compared with respect to their effectiveness and efficiency of performance. Some open problems in the area of reputation and trust-based system within the domain of wireless self-organizing networks are also discussed.