The magnetic properties and propagation of electromagnetic waves in magnetic nanoparticle systems strongly depend on the interactions between the nanosize elements having finite separation. Several aspects of the role of the dipolar and exchange interactions are reviewed on model periodic 2D and 3D magnetic nanostructures. Experiments and theory expose the critical role of proper calculation of dipole fields and statistical distributions. The control and optimization of interactions is illustrated on an example of hexagonal Permalloy ellipse arrays. The competing particle and array anisotropy, leading to a spin reorientation phase transition in Permalloy nanowires, is demonstrated. Finally, the effect of the system configuration on the interactions with electromagnetic waves is shown for ferrite and metal magnetic nanosphere arrays, demonstrating specific nanomagnetic effects, as a transition from insulator to metal, and early onset of nonlinearities.