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In this paper, we study the problem of utility maximization in P2P systems, in which aggregate application-specific utilities are maximized by running distributed algorithms on P2P nodes, which are constrained by their uplink capacities. This may be understood as extending Kelly's seminal framework from single-path unicast over general topology to multi-path multicast over P2P topology, with network coding allowed. For certain classes of popular P2P topologies, we show that routing along a linear number of trees per source can achieve the largest rate region that can be possibly obtained by (multi-source) network coding. This simplification result allows us to develop a new multi-tree routing formulation for the problem. Despite of the negative results in literature on applying Primal-dual algorithms to maximize utility under multi-path settings, we have been able to develop a Primal-dual distributed algorithm to maximize the aggregate utility under the multi-path routing environments. Utilizing our proposed sufficient condition, we show global exponential convergence of the Primal-dual algorithm to the optimal solution under different P2P communication scenarios we study. The algorithm can be implemented by utilizing only end-to-end delay measurements between P2P nodes; hence, it can be readily deployed on today's Internet. To support this claim, we have implemented the Primal-dual algorithm for use in a peer-assisted multi-party conferencing system and evaluated its performance through actual experiments on a LAN testbed and the Internet.