This book constitutes the refereed proceedings of the Third International Workshop on Self-Organizing Systems, IWSOS 2008, held in Vienna, Austria, December 10-12, 2008. The 20 revised full papers and 13 revised short papers presented were carefully selected from the 70 full and 24 short paper submissions from authors from 33 different countries. The papers are organized in topical sections on peer-to-peer systems, overlay networks as well as resource and service management.