About 4 months ago I had the front brake pads on my 2000 civic ex replaced and the rotors turned. As soon as the 90 day parts & labor warranty expired I began to notice a clicking noise in the brakes whenever I go to stop. Anybody have any idea what may cause this?

Loose bolts may, is it a click or a thump. I'm guessing bolts may have come loose. They probably didn't use threadlocker. Either that or its something else on the car. Not sure since I'm just guessing

It is definitely a clicking sound not a thumping. I think I have ruled out the possibility of it being a bad cv joint or suspension issue through testing it... It only makes the noise when the front brakes are applied. This weekend I took it to a big empty high school parking lot and let it coast to a near stop and then used the e-brake instead of the brake pedal to stop the car, neither time did it make the noise.

Well check and make sure everything is tight. Also it may be the rotor was just settling etc. whens the last time the brakes were bled