Yea, I got my Accord with 97,000 miles, and it runs extremely good. The transmission on mine is fine (auto like I said before).

-$tanley

 

I think you will find more than a 2-3 mpg difference in mileage between an AT and MT '06 Accord. I have an '06 EX-L 4 cylinder MT5. The car has about 40k miles on it. I purchased it with just over 30k. This past summer I averaged 39 mpg on a trip that was mostly highway driving. The worst mileage to date is about 28 mpg mostly around town in the middle of winter; temps in the teens and 20's fahrenheit.

I agree with the other comments already expressed regarding driveability. Driving an MT is a more engaging driving experience. Having driven MT equipped vehicles most of my life, I would also add that engines last longer as do brakes.