Well I live about 3 miles from the downtown area. Atlanta is a very heavy train traffic area. Unfortunately, the best way to see that side of Atlanta is by car. However there are some exceptions. If you take the North-South Marta line (Doraville/Airport) South to the Doraville station, it will overlook a NS yard, in Chamblee, GA with moderate traffic. Next, if you take Marta North to the Fort McPherson station, you are within 3 feet of another big NS yard heavy traffic here. Marta travels parallel to these tracks for about 5 miles. In terms of a museum, there is one north of the city about 15 miles. It’s a nice, but small museum featuring a short ride in a Southern switcher on a small track in a push/pull formation. It’s entertaining for a little while, but its definitely aimed for the younger crowd.
The Crescent arrives into the city at 900am in the morning and 730pm at night. Unfortunately the station is not extremely accessible without a car. You can take a Marta bus there, but there is not a Marta station within walking distance.
The longest, and what I consider the best route, is the North-South line. There is one other line, and another branch. The East-West line can be accessed in Downtown at the 5 Points Marta station. Not a big fan, but not a bad line at that. The branch line is rather boring. It breaks off after the Lindberg station and heads along the highway out into the burbs' a bit. Pretty boring.