Check your brake caliper bushings
Last year I did a complete front-end rebuild: rotors, calipers, hubs, bearings, U-joints, everything new. A few weeks ago I noticed a rhythmic clunking coming from the front end. I climbed under there and saw that one of the tubular rubber bushings on the passenger's side caliper had vanished (the bushings are where the guide bolts and sleeves fit). The caliper was loose and crooked on the rotor under braking. This, of course, put a drag on the rotor, which made a lot of heat, and warped the new rotor. The warped rotor moving against the loose caliper was causing the clunking. Driving like this also apparently put a lot of strain on the bearing, because when I pulled the wheel and removed the large center nut to take the assembly apart, the rotor and outer shell of the bearing fell off into my lap without being unbolted from the spindle. The bearing was ruined. All this happened within the span of about 20 miles on a single trip.
Fortunately, everything but the hub/bearing was still under warranty with the parts store, and they cut me a break on the bearing (1/2 price) because of the stupid nature of the failure. They couldn't give me just a new rubber bushing, so I got a new caliper, pads, rotor and hub bearing for about $120. Put it back together and all is well again.
One thing I added--a small washer under the head of the caliper guide bolts to retain the rubber bushings. Why they made the bolt head the same diameter as the hole in the bushing, I can't say, but a $0.01 washer cures the problem.
Anyway, next time you're under there, make sure those rubber bushings are still in place. I caught one of the others about 3/4 of the way out shortly after the first one went missing.
Hope this helps someone else.