I'm no mechanical genius, but I have 2 2k Accords, so i'll give you my 2 cents worth.
First - your car is about 4 years old with only 16k miles (4k per year - very low). Was this recent body damage or did it happen 3 years ago and the car has been sitting since then? Regardless, you may want to just refresh all your fluids because of their age. Oil, trans fluid, brake fluid, coolant, even windshield washer fluid - I would drain and replace all of them to get a fresh starting point for the car.
Carefully inspect the tires for uneven wear or rubber cracking, then drive it at different speeds to check for vibration from out of balance wheels, out of alignment, or flat spots on the tires. This car has been sitting a lot. Also, a severe rear end hit could throw off the alignment or wheel balance.
The trans - because of the inherently bad design of the auto trans in the 6th gen Accords, you have a 50/50 chance of having the trans crap out on you. Honda has graciously extended the trans warranty to 7 yrs / 100k miles for the 2000 and 2001 Accords, so you will have 3 years to figure out if yours will be one of the failures. Don't worry - you will get a free replacement if it happens in the 7/100 window.
Note - if the car was in "Park" or even "Drive" when it was smashed from behind, that could have really jolted the trans, and may have caused some damage. Don't be too quick to tell the Honda dealer this car was an accident repair or they may not honor the trans warranty.
After 4 years the a/c cabin filter is probably dirty and stale smelling. You can replace this yourself for the cost of a pair of new filters - roughly $20 - $25. Search for the instructions here or on other sites.
I know the 2000 LX came without a standard CD player in the head unit. If you don't have one in your 2001, you can pick one up on EBay for about $50, and installation is simple.
One last item - there was a general recall on the 2000 and 2001 Accords for replacement of the ignition switch. Check with your local dealer to see if your car is affected.
Happy driving...!
