Do the lights pulse in time with the engine? I other words, if the engine speeds up, does the pulsing speed up as well?
If so, then it sounds like your alternator has lost a diode (or two - there are six inside). That would produce a noticeable 'hump' in the output voltage. In fact, your voltmeter on the dash may show lower than normal voltage, especially with the headlights on - the voltage regulator can compensate a bit for the reduced voltage of a broken diode, but not at full load.
If, instead, the lights are pulsing randomly, then it's likely a loose connection. Either something simple such as a battery or ground wire to the alternator, or something internal to the alternator (voltage regulator pack is loose or corroded.
Try cleaning/reseating the connections to the alternator. If that doesn't work, then have the alternator tested.