Vibration when braking usually comes from an uneven deposit of brake pad residue on your rotors. This is generally known as "warped rotors", but the rotors themselves don't really warp. This can happen from overheating the brake pads followed by a cooling period where the car was parked, instead of moving. An example would be heavy braking coming off a freeway ramp, then parking the car shortly after. When the brake pad cools down on the rotor, brake pad material can be deposited, creating a "sticky" spot. So the next time you drive the car, the brake pads contact the rotor in both the "smooth" and "sticky" sections, which causes this vibration. This doesn't matter how much brake pad material you have left.
Stoptech has a great write up on this.
http://www.stoptech.com/technical-support/technical-white-papers/-warped-brake-disc-and-other-myths
I've experienced this first hand on my wife's 2010 Accord. I was coming off a freeway ramp which required fairly heavy braking. I could tell the pads were heating up because the stopping power got weaker and weaker even as I applied more brake pressure (brake fade). At the end of the freeway ramp was a stoplight, where I had to wait for a couple minutes. This means the overheated brake pads were only contacting one spot of the rotors and being pressed against them, depositing a bit of pad material on the rotor. Immediately after this freeway ramp, the next time I used the brakes, I could feel a slight vibration through the pedal. It continued to get worse over the following days and was only rectified after I got the rotors resurfaced.
Like others have stated, if you feel the vibration more through the steering wheel, it's most likely the front rotors. If you feel it mostly through the pedal, it could mainly be the rear rotors. Regardless, if you still have a good amount of brake pad life left, resurfacing the rotors (or replacing) should fix the problem. Then be weary of your driving habits to not over heat the brakes or give sufficient cooling time before parking the car. If you live in an area that is very hard on the brakes, you can consider upgrading to a higher performance brake pad material that has a higher operating temperature so it's less susceptible to overheating.