Atlas Trainman cars are scale, but have molded-on details in some areas. I have several. They do, however, use the same trucks as the Masterline cars and have pretty good weight.
MTH Premier cars are generally scale with the exception of the passenger cars which are only 72-feet instead of 80-85 feet. Some of them, however, are in fantasy paint schemes but that only matters when the "rivet-counting" eventually sets in.
MTH Rail King cars are usually smaller than scale, though there are some exceptions that are scale models of smaller prototypes. Some cabooses were former Premier tooling and are scale sized. Your best bet here is to know the prototype information when selecting a freight car.
Lionel is a bit of a wild card, but the high-end freight cars have moved toward scale and it usually says so in the catalog. A couple of very popular freight cars are the new 89-foot auto racks, the 86-foot excess-height box cars, and the PS-4 flat cars (a lot of those ended up in the hands of our 2-rail colleagues and got converted). By the way, if you want scale-length passenger cars, Lionel is capitalizing on their new tooling and have been releasing them in several road names (the consists are generic and not necessarily road-specific).
Weaver cars are pretty plentiful on eBay and are scale. Most of them are too light and need to have weights added. Invest in a digital postal scale and some half-ounce stick on iron wheel weights (both available on eBay for reasonable prices). NMRA weight standard is five ounces, plus one ounce per inch of car length so a 40-foot box car (10") should be at 15 ounces. The cars will track much better.
Hope this helps some.
