We present a rather general and efficient method of simulating electron-spin echo spectra for spin systems where the microwave frequency does not simultaneously excite EPR transitions that share a common level. The approach can handle arbitrary pulse sequences with microwave pulses of arbitrary length and strength. The signal is computed as a sum over signals from the electron coherence transfer pathways contributing to the detected echo. For each pathway, amplitudes and frequencies of the signal components are computed and used to construct a spectral histogram from which the time-domain signal is obtained. For multinuclear spin systems, the nuclear subspace is factorized to accelerate the computation. The method is also applicable to high electron spin systems with significant zero-field splitting and to pulse electron-nuclear double resonance experiments. The method is implemented in the software package EasySpin, and several illustrative calculations are shown.