TMB
Between Atlas, Lionel, MTH and Weaver you have dozens of types of box cars and literally hundreds of paint schemes to chose from. To make it a little easier let's break things down by car length and era.
First, you have 40 foot cars that were built from World War I until the 1930s. These cars were lower and narrower that the cars that were built from the late 1930s on and typically had only a 40 ton load capacity. While these cars were constructed before locomotives like the UP FEFs they continued in use until the end of steam and into the diesel era.
The USRA box cars were built at the direction of the US government to a standard design with steel underframes and ends. Similar cars were built for many railroads in the 1920s. They came in both double wood sheathed and single sheathed/outside steel braced versions. Atlas, Lionel and MTH all made a double sheathed box car. I think the MTH version is the best model. Atlas and MTH make very closely comparable single sheathed USRA box cars.
These two USRA box cars are from MTH.
Weaver makes a single wood sheathed/outside steel braced box car that I believe represents an early 1930s prototype with more modern steel ends than the USRA cars.
Atlas makes two box cars that represent early steel sided cars. One is a USRA car rebuilt with steel sides and the other is the X-29, a Pennsylvania Railroad design.
The box car designs from the World War I era through the early 1930s have dimensions that are close to what we we might think of today as O-27 box cars. While they are 40 scale feet (ten inches) long their lower height and narrower width make them look quite small when compared to the designs that followed. The models listed above are all quite detailed when compared to a 6464 box car even though there overall dimensions are not very different.
In the late 1930s railroads and car manufacturers introduced several designs of 40 foot box cars with greater interior height and width. Fifty ton load capacity became the norm around this time. The most common design was adopted as standard by the American Association of Railroads in 1937. These are referred to as 1937 AAR box cars. Atlas and MTH build slightly different versions of this car. Both have the common dreadnought steel end. Atlas uses the more typical Murphy rectangular panel steel roof and the MTH car features a Viking steel roof. Atlas builds their 1937 AAR box cars in both single and double door versions.
MTH
Atlas
Some railroads built cars to their own design in that period. Weaver sells a distinctive B&O "wagon top" box car that features sides that curve into the roof without eaves. The Pennsylvania came out with their own X-31 round roof design and Lionel has announced but not yet delivered a model of this car. Weaver has also announced a model of the Milwaukee Roads rib side box car that is anxiously awaited.
After World War II slight evolutionary changes came to car construction. Advances to end and roof stamping offered increased strength and weight savings. The Atlas Trainman 40 foot box car is a model of a Post War built standard design cars with improved dreadnought ends and a diagonal panel roof.
Pullman-Standard came out with their own line of cars that featured distinctively shaped proprietary end and roof stampings and made extensive use of welded construction for additional strength and weight savings. The Lionel model of the PS-1 40 foot box car is a very fine model and is discussed on
this thread. Weaver also offers a 40 foot PS-1 car and the early MTH premier 40 foot box car is a model of the PS-1 although it was not advertised as such. Both the Weaver and MTH models are less detailed that the Lionel PS-1 but are usually priced accordingly.
The Weaver PS-1
Fifty foot box cars were also common in the late steam era.
Many 50 foot box cars were built in the 1920s, 30s and 40s to transport automobiles.
Atlas offers a single sheathed/outside steel braced box car in their Trainman Line. According to Model Railroader it is based on a car built in the late 1920s by Pullman for the Western Pacific. I have several lettered for the CB&Q, GN and NP although the sides, roof or ends are not correct for these roadnames. They are distinctive and add variety to a train by depicting big car of modern dimensions dimensions with older style construction.
Many automobile box cars had opening doors on one end in addition to double doors on each side. MTH offers a 50 foot all steel double door box car with non-opening end doors. Lionel has built 50 foot automobile box cars with plain ends or with end doors that actually open.
MTH
Lionel
Pecos River also offered 50 foot box cars with pain ends or functioning end doors. They can still be found at shows or for sale in on line auctions. The Lionel cars are nicely detailed. The MTH cars have had detail upgrades since they were introduced in the late 90s. The Pecos River cars have a lower detail level, about like Atlas Trainman cars.
Pullman-Standard also built PS-1 box cars as 50 footers. Atlas offers 50 foot PS-1 box car models with single sliding doors, double sliding doors or a single plug door. Many of these models carry paint schemes that are a little too modern for the end of the steam era. However, early PS-1 box cars, even the 50 footers, were coming off the production line when steam was still hard at work.
Both
Lionel and MTH have good product locator features on their web sites. Here is a link to MTH Premier
Union Pacific Box Cars. Atlas doesn't allow you to search by roadname but they have offered several steam era UP box cars. And of course UP trains would have had cars from many other railroads in them.
I hope that helps, even if it doesn't narrow things down very much. If you want to add some scale reefers to your collection there are almost as many options!