I'm no expert on the subject, but I know they use a new type of bearings (FDB?) which helps a lot. All I know is I love how quiet they are, I have 6 hard drives and I can't even hear them over my quiet fans.
Fluid dynamic bearings are one reason. Exceptionally old hard drives didn't have the voice-coil servo-guided head mechanism they have now, they used a noisier stepper motor.
But the main reason drives are quieter now is the acoustic management algorithms now implemented in the servo controller. Instead of driving the voice coil with full current to move it immediately from track to track (which caused sudden stops/reverses and overshoots which make noise), modern HDs use a ramp-up/ramp-down of the current profile to provide a gentle acceleration/deceleration of the head. This can reduce head seek noise to very low levels.