Looks like SCARM has American Flyer and Lionel American Flyer in S and is free. Very nice program, has excellent 3D views.
Anyrail is another you can try out and will allow the use of up to 50 pieces of track for trial. You have to purchase the program to use more than 50 pieces of track. Not sure about the S gauge libraries it has?
RR-Track is pay, but has many more track libraries, example plans and accessories. Some track libraries, accessories and example plans may be extra cost. Been around a long time also. RR-Track advertises in OGR magazine.