I am experiencing something similar....
Whenever I hit the gas, I hear a knock, normally only in 1st or 2nd gear. It only happens from the stock to go, or when I am going like 35mph+ in 2nd gear, and hit the gas hard to like rock the car.
I just had my stereo apart, so it may just be something loose, but it sounded like it was coming from the tranny....
I haven't been too rough with the car, considering its a 2001 I'm hoping its not a transmission prob...