I've had this problem since I bought the car a year and half ago...just seeing if anyone else has had this. I notice it more in the winter since the car doesn't shut off at stoplights as much.

Its not real violent but I have had 4 other Hondas (three Civics and a 98 Accord V6 that we still have) and none have had the shakes this much. Its when I am at a complete stop, but in Drive with engine running of course. If I put it in neutral it pretty much goes away.

Its been to the dealer multiple times and they have basically told me it is normal and I am crazy. They did change the flywheel and all the engine mounts as a "courtesy" or whatever Honda calls that.

I noticed it after they changed the starter clutches right after I bought the car used (at 87K miles) though that may not have been the cause, we just may not have noticed it as much since we hadn't had it that long.