The shipping industry is essential for international trade. However, in the wake of the 2008 financial crisis, this industry was severely hit. In these times, transportation companies can only obtain profit if their fleet is routed effectively. In this work, we study a class of ship routing problems related to the Pickup and Delivery Problem with Time Windows. To solve these problems, we introduce a heuristic and an exact method. The heuristic method is a hybrid metaheuristic with a set-partitioning-based large neighborhood, while the exact method is a branch-and-price algorithm. We conduct experiments on a benchmark suite based on real-life shipping segments. The results obtained show that our algorithms largely outperform the state-of-the-art methodologies. Next, we adapt the benchmark suite to model a ship routing problem where the speed on each sailing leg is a decision variable, and fuel consumption per time unit is a convex function of the ship speed and payload. To solve this new ship routing problem with speed optimization, we extend our metaheuristic to find optimal speed decisions on every local search move evaluation. Our computational experiments demonstrate that such approach can be highly profitable, with only a moderate increase in computational effort.