I'm doing some work in Logic, and right now I'm messing around with some bass. I've gotten to a point where my headphones actually vibrate somewhat, like a tiny massage on the sides of my head.. Is that harmful toward me or the headphones?
In general, you should be very careful how loud you listen to music, both through headphones and through speakers, so you do not damage your hearing. You should be listening at the lowest level that still allows you to hear what you need to. Listening at higher volumes for short periods will allow you to better hear the nuances of the music, but should be kept to an absolute minimum.
If the headphones are vibrating with the bass, they are probably really good at reproducing the lower frequencies. If you are not hearing any distortion, you are probably not damaging the headphones, but it is still possible that the excess vibrations will cause damage over time.
In general, when in doubt, turn it down a bit.