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We investigate modulation schemes optimized for two-way wireless relaying systems, for which network coding is employed at the physical layer. We consider network coding based on denoise-and-forward (DNF) protocol, which consists of two stages: multiple access (MA) stage, where two terminals transmit simultaneously towards a relay, and broadcast (BC) stage, where the relay transmits towards the both terminals. We introduce a design principle of modulation and network coding, considering the superposed constellations during the MA stage. For the case of QPSK modulations at the MA stage, we show that QPSK constellations with an exclusive-or (XOR) network coding do not always offer the best transmission for the BC stage, and that there are several channel conditions in which unconventional 5-ary constellations lead to a better throughput performance. Through the use of sphere packing, we optimize the constellation for such an irregular network coding. We further discuss the design issue of the modulation in the case when the relay exploits diversity receptions such as multiple-antenna diversity and path diversity in frequency-selective fading. In addition, we apply our design strategy to a relaying system using higher-level modulations of 16QAM in the MA stage. Performance evaluations confirm that the proposed scheme can significantly improve end-to-end throughput for two-way relaying systems.