Integer programming (IP) has proven to be highly effective in solving many path-based optimization problems in robotics. However, the applications of IP are generally done in an ad-hoc, problem specific manner. In this work, after examined a wide range of path-based optimization problems, we describe an IP solution methodology for these problems that is both easy to apply (in two simple steps) and high-performance in terms of the computation time and the achieved optimality. We demonstrate the generality of our approach through the application to three challenging path-based optimization problems: multi-robot path planning (MPP), minimum constraint removal (MCR), and reward collection problems RCPs). Associated experiments show that the approach can efficiently produce (near-)optimal solutions for problems with large state spaces, complex constraints, and complicated objective functions. In conjunction with the proposition of the IP methodology, we introduce two new and practical robotics problems: multi-robot minimum constraint removal (MMCR) and multi-robot path planning (MPP) with partial solutions, which can be quickly and effectively solved using our proposed IP solution pipeline.