I would start with cleaning the rims like mentioned above and maybe a light sanding on your brake pads. It is less likely but an extremely worn out rim can cause pulsing if the brake track has worn so thin it is causing the rim to bulge in spots. That would also mean your rim is beyond the point where you should have replaced it. Usually with lighter weight rims, after you have worn .5mm or so off the brake track they are due for replacement. You would also notice the brake track feels very concave.