In this paper we illustrate a new methodology for the design of fault-tolerant logical topologies in wavelength-routed optical networks exploiting wavelength division multiplexing, and supporting both unicast and multicast IP datagram flows. Our approach to protection and restoration generalizes the "design protection" concepts, and relies on the dynamic capabilities of IP routing to re-route IP datagrams when faults occur, thus leading to high-performance cost-effective fault-tolerant logical topologies. Our approach to protection and restoration for the first time considers the resilience properties of the topology during the logical topology optimization process, thus extending the optimization of the network resilience performance also on the space of the logical topologies. Numerical results clearly show that our approach outperforms the previous ones, and is able to obtain very good logical topologies with limited complexity.