What a daunting task to list everything. Below are some guidelines.
Any EMD locomotive from the GP38-2/SD38-2 (the SD38-2 was not built in significant numbers) and later (replace the 38 with a higher number, some do not have the -2, like the GP60) and any GE locomotive with -8, -9, AC, or ES in the designation will still be very common on Class 1s. GE -7s may still used by Class 1s in fairly significant numbers. EMD SW1500s, MP15/MP15DCs, and MP15ACs are probably also significantly used by Class 1s. For shortlines, generally any four axle (espicially EMD) locomotive could be believeable, although second generation locomotives are displacing large quantities of the first generation locomotives on many shortlines.
Boxcars/Reefers: no roofwalk, low brake wheel (there are still some real boxcars with high brake wheels running around). Almost all boxcars built within the last 15 years are excess height with the majority seeming to be 60’ interior length, though there are still thousands from the 60s, 70s, 80s, and even 90s that are not excess height.
Flatcars: generally, look for a minimum length of 54’, even that does not guarentee a modern car. For TOFC flatcars, 89’ is the minimum length. Any spine-cars (excluding Impack [sic], at least I have never seen any) and double stack cars are still in use. Any fully enclosed autocarrier would still be around.
Covered hoppers, look for rooftop walkways toward the sides of the car, not down the center. I believe that the Airslide hoppers have their walkway down the middle of the roof and they were made into the 1990s, so they are an exception.
Open top hoppers, looking at the trucks would probably be the most reliable way to determine if it is modern. Walthers 4-bay, aggregate, and Ortner; Bowser 3-bay; Athearn rapid discharge all are modern. The Atlas Trainman car looks similar to modern cars but those are probably all out of service by now.
Gondolas, most modern