Like motive power, the different operating eras and schemes require more rolling stock than would normally be included on a model railroad this size.  Unlike motive power, I won't have separate rolling stock rosters for each operating scheme.  Instead, I plan on using the same mid-60's equipment for all of the mid-60's operating schemes and the same mid-80's equipment for all of the mid-80's operating schemes.  The exception being the cabooses, which will be different between the different roads and eras.  In the meantime, until I get a chance to collect and/or setup all of the necessary equipment, engines and rolling stock will be used in different operating schemes.
 
With one or two exceptions, rolling stock will be kept at 40 scale feet or shorter.  This is because shorter rolling stock (and motive power, for that matter) looks less out-of-place on a small layout going around tight curves and fitting into short spurs.  Shorter cars also make for shorter trains, which also looks less awkward on a small layout, and allows more to fit in the passing siding.
Every car that I run on the layout uses Micro-Trains trucks, couplers and low-profile (small flanges) wheelsets.  The trucks are used because they work the best on my layout, and because most of my couplers are truck mounted, so I need them to use the MT couplers.  The  couplers are used because I have found them to be the only couplers that work for delayed uncoupling.  The low-profile wheelsets are used both for looks (they eliminate the "Mini-Lionel" look of the "pizza cutter" wheelsets), and because you need them to run the cars on the code 40 rail spurs.  With the smaller flanges, the cars are more apt to derail, especially during certain switching moves.  But I've found that adding weight to the cars mostly eliminates that problem for me.
 
I also install Micro-Train's restraining springs on one axle on each car.  Initially, I did this to keep the trains running smoothly (eliminating the bouncing accordian effect, whether the caboose is connected or not), but I also found that the cars will stay put on the grades as if brakes were applied, which allows me much more flexibility when I am switching cars around.   The combination of extra weight and restraining springs on the cars obviously makes them harder to pull up grade, which decreases the number of cars a single engine could pull around the layout.  But this is hasn't been a problem, because the trains are normally short enough to begin with, and it's not a problem to double up engines when the train is long enough.

At this time, I do not expect to be adding Z couplers to any of the cars, except maybe the cabooses.  I still have to figure out how I would want to convert the cars, and the trucks are easily removed for changing the couplers if I want to add them down the line anyway.  I keep the couplers truck mounted for the most part, because they normally work better around the tight curves.
Some cars like the coal hoppers will remain the same between the different eras, while items like covered hoppers and boxcars will be updated between the different eras.