Do you have an example? What midi synth and what processor are you using? In any case, if I understand what you have in mind, what you need is a bunch (or at least two) oscillators (not sines, you'll need stuff with a lot of harmonics, e.g. one triangle and one square wave, not perfectly tuned with each other), low pass filter (with resonance not cranked up all the way to self-oscillation) and LFO modulating filter cutoff. The shape of the LFO gives you the type of throb. Saw gets you a more rhythmic/percussive throb, while triangle and sine gives you a more pulsating throb, and ramp( upwards-sloping saw) gets you a "reverse" throb. Feeding the output of the filter into the filter itself can help you get a partially overdriven tone.
HTH. If any of this is unclear, I am willing to explain it better.
