Current research directions in semantic peer-to-peer (SP2P) networks are evolving to combine two complementary technologies: peer-to-peer (P2P) networks and formally structured information (ontology). SP2P systems represent the next step in the evolution of P2P networks because SP2P systems incorporate several additional features not present in P2P networks. Ontologies are advantageous in P2P networks because they provide the possibility for improving search and content retrieval. The current SP2P research efforts have generated many and diverse realizations and architectures. This diversity in implementation and architecture in turn has led to an ambiguity and incompatibility in defining domain abstracts and concepts. Progress in this area is hampered by a lack of commonality between these approaches, which makes their comparison and translation into practical implementations difficult. In this study, we describe a reference model for SP2P systems in an effort to model the emerging decentralized computing paradigm in a generic and high level abstraction. An SP2P simulation framework based on the reference model has been built. The framework is generic which enables instantiating different existing SP2P systems. A particular system can be considered an instance of the framework. This facilitates examining the effect of architecture changes, i.e., introducing different component implementations, on the behavior of the existing system. Further, the framework enables testing newly developed solutions to existing problems in SP2P systems. Simulation models are derived from the framework for studying the lack of fault-tolerance in the current SP2P systems. Two novel solutions are developed for reliability problem in the SP2P systems, and the effect of the developed solution on existing SP2P system behaviors are studied.