Vibration while stopped at a light, in Drive

2000 Mazda 626 4cyl, 2.0 ltr, 133,000 miles
I recently had to use on of those tire donuts when a front tire went flat. I drove about 30 miles to a service station.
After the tire was replaced, I noticed a rough vibration when in "drive" while stopped at a light. Shifting to neutral stopped the vibration.
Two weeks later, yes I know I should have taken it in right away, it is vibrating in all gears but moreso in drive and reverse, when stopped. It seems to run fine when the car is moving more than 5 miles an hour.
Any ideas?