We're frequent travelers on Amtrak but the regular train, not the AT but are quite similar....
We travel coach mostly (sleepers are ridiciously priced) and we take a cooler....we freeze lemonade, and use it for the coolers ice, have sandwiches and snacks....pickles, tomatoes etc. and bulid our sandwiches right in the coach seats, have our drinks and enjoy.....yes, Club Car food is expensive and very limited in choice....dinner car is way over priced but meals are decent quaility wise.....
We take blankets, horseshoe pillows.....Ipods, gameboys, Kindles, puzzle books and personally myself a handheld GPS, to see exactly where we are...and our cameras..just remember to use earphones...we never leave anything of value in our checked bags and also don't leave anything in our seats either of value....we never go to the Club Car or Dining Car together, so one stays behind to watch our stuff.....I also like to take some earplugs and eye masks along for just in case....don't take up much room and can mean the difference in a trip....
We pack one rolling duffle each, which usually goes in baggage (limit 50#'s) and we have one carryone each plus cooler and munchie bag.....where we board, 3 am is an unmanned station so no baggage car access....but there is ample storage in the coach cars for luggage....
We take to our seats whatever is going to occupy our time with, most goes in the overhead and what we're using the most is at our feet.....we have the lemonade to drink as it thaws, plus some frozen bottled water too......bulk of our travelings is in the luggage car......we try to keep it simple.....