Heterogeneous servers are becoming prevalent in many high-performance computing environments, including clusters and datacenters. In this paper, we consider multi-objective scheduling for heterogeneous server systems to optimize simultaneously the application performance, energy consumption and thermal imbalance. First, a greedy online framework is presented to allow the scheduling decisions to be made based on any well-defined cost function. To tackle the possibly conflicting objectives, we propose a fuzzy-based priority approach for exploring the tradeoffs of two or more objectives at the same time. Moreover, we present a heuristic algorithm for the static placement of physical machines in order to reduce the maximum temperature at the server outlets. Extensive simulations based on an emerging class of high-density server system have demonstrated the effectiveness of our proposed approach and heuristics in optimizing multiple objectives while achieving better thermal balance.