This paper presents an integral equation formulation specialized for the analysis of capacitive waveguide circuits, which include arbitrarily shaped conducting and homogeneous magnetic/dielectric objects. The technique benefits from the symmetry of the structure by formulating a two-dimensional scattering problem with oblique angle of incidence, combined with the use of the parallel plate Green's functions. As practical applications, the paper proposes novel lowpass filter designs loaded or coated with dielectric and magnetic homogeneous materials. If the filter is properly designed, the use of these materials could improve the filter response, selectivity or out of band performance, and power handling capabilities. Some novel filter design implementations, showing these kind of benefits are presented for the first time in the paper. For validation, a commercial full-wave simulator is employed, showing the validity, accuracy and computational efficiency of the novel software tool.