This paper deals with three-dimensional effects in tokamaks that can be approximated by slowly varying 3D equilibria so that their theoretical description and corresponding code developments can benefit from stellarator research. We investigate the effect of magnetic field ripple and magnetic islands on fast particle orbits and find a strong synergistic effect. The coupling of the plasma perturbation to realistic tokamak wall structures introduces 3D elements into the treatment of resistive wall modes (RWMs). We have developed and successfully benchmarked an RWM code allowing for 3D plasma equilibria and wall geometries. We show that for realistic wall structures the 3D effects remove the degeneracy of +/- n modes and can give rise to significant coupling of modes with different toroidal mode numbers n. Kinetic damping of RWMs by plasma rotation is investigated in the low rotation regime relevant for ITER and DEMO. It is found that the inclusion of drift wave physics results in an increased damping for plasma rotation velocities in the range of the diamagnetic frequency due to the resonant excitation of electrostatic plasma waves.