In this thesis, we address two challenges: solving multi-objective integer programs and solving large-scale transportation problems. In Chapter 2, we present a novel fast and robust algorithm for solving bi-objective mixed integer programs that extends and merge ideas from two existing methods: the $\epsilon$-Tabu Method and the Boxed Line Method. In Chapter 3, we study a new service network design problem in which the number of vehicles that can simultaneously load or unload at a hub is limited. We propose a non-trivial integer programming model for solving the problem, and, to be able to solve real-world instances, we design and implement two heuristics: (1) a metaheuristic, and (2) a hybrid matheuristic. In Chapter 4, we introduce a nove...