The wavelength-routed optical network-on-chip (WRONoC) is a promising solution for advanced signal communication because of its high-bandwidth, low-latency, and power-efficient signal transmissions. Existing WRONoC topology designs rely on pre-defined network templates with limited solution space and design purposes. To remedy these disadvantages, we present a general model for WRONoC topologies. Based on this model, we propose a novel design flow for customized and fault-tolerant topologies to minimize the maximum insertion loss and the wavelength and micro-ring resonator (MRR) usage. Besides, we present two fault-tolerant topologies for full-connectivity netlists, namely the Actin-STAR and Zygo-STAR topologies. We prove that the Actin-STAR topology has a performance bound of 2.22 in the primary-path maximum insertion loss, and the Zygo-STAR topology has a performance bound of 1.39 in the backup-path one. Experimental results show that our designs significantly outperform the state-of-the-art designs in wavelength, MRR usage, and maximum insertion loss.