There are a few things you could try. First, if you didn't break in the pads and rotors properly, one or both may have glazed. Meaning, either the pad became smooth because of excessive heat, or the rotor did. To fix that, sand the mating surfaces with sandpaper. This isn't to make the surfaces smooth, so pick something like 80 or 100 grit. Second, you may want to make sure that you tightened your calipers enough. Too loose, and they'll vibrate, which would be heard as a moan or knocking, depending on how loose they are. Third, if all else fails and it really bothers you, try a softer pad. However, this will mean alot more brake dust on your rims. Slotted and/or drilled rotors are like cheese graters for brake pads.
Oh, and also check that your dust guards aren't rubbing on your rotors. I had that problem once on another car, and it sounded like a cat was caught in my serpentine belt.