get new rotors and make sure they're fitted correctly - no rust under
the hub, then, and this is the most important part, /make sure the lug
nuts are torqued correctly/.  hondas have lightweight hubs.  incorrect
torque procedure leads to local distortion and the problems you
describe.  make sure the lug nuts are tightened by a hand torque wrench,
NOT air tool with a 1324, 1324 or 13524, 13524 two [or more] stage
process, the first one with the wheel off the ground.

after that, you'll never experience this problem again.  i've taken
hondas to the shop with good brakes and driven them home with badly
pulsing brakes because of incorrect process.  re-torque the wheels on
arrival at home and the problem disappears again.  you probably won't be
able to do this because if used in this condition too long, the rotors
wear unevenly.

you can change the rotors yourself if you want.  it's simple to do and
the rotors aren't very expensive.

Anyone have any ideas how I can remedy this problem?  I have a 2001
Accord LX V6 that has given me brake problems since it had 40,000 miles
on it.  I currently have 80,000 and every 15K or so the car starts
pulsating when braking.  Each time I've brought it in to the local shop
I use they tell me the rotors are warped.  I've put new ones on the
front and back since the originals were machined twice.  I also had to
get new pads at 40K and nearly all my driving is highway.

My wife has a 2002 Civic and I had a 93 Civic with no problems.  Am I
doomed to suffer brake issues until I get rid of this car?  I typically
get 60 to 70K out of a car before I need new pads and machined rotors,
but this Accord is an exception.