Self-propelled particles are a class of far-from-equilibrium systems which present many complex, emergent features that are not obvious from the microscopic dynamics. Simulations of well-chosen instances of such systems are a powerful yet tractable method of investigating many real-world phenomena. The frequently non-time-reversible interactions of many cases of self-propelled particles with surfaces means that the environment has an impact on large-scale behaviour in a way that would not be true for particles close to thermal equilibrium. This work investigates several examples of such systems, and compares them with experimental results for comparable systems: firstly, the spatial distribution of smooth-swimming mutants of Eschericia Coli within water-in-oil emulsion is investigated, and its dependence on inter-bacterial interactions and the size of water droplets. The nature of bacterial collisions is inferred through data analysis and simulation. Secondly, pattern formation by chemotactic run-and-tumble bacteria due to secretion of a chemoattractant by the bacteria themselves, demonstrating a range of approaches to control the formation of biofilms by bacteria. Finally the dependence of the bulk transport properties of chemotactic self-propelled particles in porous environments, on their detailed dynamics, is probed: how they interact with obstacles, their form of chemotactic response, their ability to actively enhance their rotational noise, and their method of sensing chemical gradients.