One of the priorities with this layout is to include as much operation as possible on this small layout.  One method I employed during track planning was to squeeze in as many spurs as practical, and as long of a mainline run as practical to further separate those sidings "as the track runs", to help the illusion of distance.
 
For variation in engines and rolling stock, I run two different "eras" during different operating sessions.  One era is mid-60s, utilizing GP7/9/20/30/35 type motive power, box cars with walkways, PS2 covered hoppers, appropriate cabooses, etc..  The other era is mid-80s, utilizing GP15/38/39/40 motive power (in addition to older versions of the other era's motive power), box cars without walkways, cylindrical covered hoppers, appropriate cabooses, etc..  Other than some vehicles, the scenery will stay the same.  Some of this won't be exactly prototypical, but I am willing to trade that for some variety in rolling stock and motive power.
 
To allow for the use of different engines and paint schemes, and to add some variation in operation, I also came up with several different operational schemes for each era.  One scheme is for the Blue Creek Railroad, which is a fictitional short line.  The second scheme is for a fictitional Dante branch of the Clinchfield Railroad.  The third scheme is for a fictitional Embreeville branch of the Southern Railway, and the fourth scheme is for a fictitional Talcott branch of the Chesapeake and Ohio Railroad.  Of course, one could simply use the same railroad, engines, and cabooses for each of the different operating schemes, if all they wanted to do was expand the variety in operating a small layout.  And in my case, I could use each railroad set for different schemes to mix things up even further.  Down the line, I expect to come up with other combinations for operating schemes, which may or may not have railroads specifically assigned to them.  
 
Each of the operating schemes utilizes at least two locals, both for variety, and because one local would be so long as to be very awkward to operate, considering the fact that a single local would be a minimum of twelve cars, which is longer than the lone passing siding.  In all of these scenarios, East is counter-clockwise, and West is clockwise.  The single passing siding on the layout represents several different passing sidings along the route, and the interchange spur on the layout represents several different interchanges.  In each of these schemes, I run the train completely around the layout one or more times to emulate distance between some locations.  A limitation common to all scenarios is that the piggyback cars do not fit in one of the tunnels.  Therefore, the piggyback cars are switched from a nearby interchange, instead of being brought along with one of the locals.
 
Most of the time, cars will simply be swapped out one-for-one at each industry.  Each industry in an operating schematic is labeled with the normal amount of cars for that industry.  For the industries with a variable number of cars, the smaller amount of cars will normally be delivered (for example, the warehouse labeled for 1-2 box cars will normally have 1 box car delivered).  But occasionally, I will add or subtract a car for variety.  In each operating schematic, each industry also has a number with a circle.  I simply roll a die for each local, and if the number comes up for an industry, I will omit one car for delivery to that industry, except for industries labeled with a variable number of cars, in which case I will add another car for that industry (for example, the warehouse would then have two box cars delivered).  In some cases, there are less than six industries covered by a local, in which case, if there are only four industries, and a five is rolled, then no cars are added or omitted from the local.  Regardless of how many cars are delivered to an industry or interchange, all cars sitting in each siding will be retrieved.
 
See the pages for each operational scheme for more information.