The further you get into model railroading, the more you learn about the cars. Some are just plain and expected (like your standard boxcar) while others take on a life of their own (like a caboose). Sometimes you find a boxcar with something unique about the markings. Depending on the railroad, you may even get an idea of when the car ran based on the logo design or marketing terms painted on them.
THis is just a page to collect my research on some of my more 'special' cars.
PGH Division #4477479(at least 1957)
American Railway Express #4988(1927-1937)
American Railway Express (ARE) became Railway Express Agency (REA)
Car was modified for express service late 1926/early 1927. By 1937, would have been renumbered and returned back to freight service. These cars were assigned to "passenger service". The trains were not actually "passenger" trains, but were made up of X29 box cars, express reefers, RPOs (Railway Post Office), B60s (baggage cars), etc. The express trains ran on a priority scheduling, just like passenger trains. 
 -- http://jbritton.pennsyrr.com/index.php/tpm/100-cabin-cars-in-express-service  -- https://railroad.net/prr-cabin-car-special-assignments-t86373.html#p979144
N5k Caboose(PC 1970-1976 & CR 1976- ? )
The N5k caboose was chopped down version of an ATSF offset-copula used as a transfer caboose. Some people consider them ugly, but I find them to be wonderful! You can see more about my project to make my N5k caboose on its own page.
Bottle Cars(unknown years)
(Not to be confused with a Torpedo car) These were some of the first cars I purchased new. I honestly had no clue what they were exactly. I just knew that for my first layout I need a number of short length gondolas, and these fit the bill. It took me a while to find out what they were since I didn't even know there were nicknamed "Bottle cars". Eventually I found that the 'bottles' are air-activated cement canisters. I don't know if they ever carried anything other than cement, and I have no clue if they were as popular as Atlas would have you believe. (Pretty sure Altas has put out one for every road name)
H30 Covered Hopper(1935-1979/early 80's )
When I first purchased these, I just thought I was getting a few covered hoppers. When I started researching, I found that these are some of the first 'dedicated' covered hoppers. Prior to 1930s, weather sensitive materials would be carried either in a boxcar, or in some converted open hoppers. A lot more details can be found in this NASG Dispatch article from Apr 1989 found on the River Raisin Model site.
Since I am modelling 1956-75 PRR/PC railways, I picked up 4 of these hoppers. Two are grey (pictured), one is PRR tuscan red, and the fourth is PC green. Original delivered as only tuscan red, then after/about the 50s delivered with the grey scheme.
These cars had a long run, lasting all the way up to Conrail days - by this time most were serving as locomotive-sanding service and 'maintenance of way'. Early on, they were mostly cement, but some even labeled "grain only".
(NYC had similar service they called "Pacemaker", B&O had "Sentinel", I assume many of major RR had their own version. ) This service was designed for "express delivery". They used equipment rated for higher speeds, and ran at passenger train speeds. Ran a fixed route with specific drop-off/pickup spots along the route,  and stayed on 'home rails'. Once the program declined, the cars found their way to general service, often without a repaint.
 -- https://forums.auran.com/trainz/showthread.php?93726-NYC-and-PRR-LCL-services&s=a7be86e33fd1a64278e4d89e259145f1&p=1046687#post1046687
PRR 50' - General American/Damage Free (late 50s - early 70s)
Picked this one up really just due to it being a 50' boxcar (I had more than enough 40' at this time) and it being a PRR look that I had not seen. It is a dark green, but not "tuscan", had "No Damage" in white, and a black "General American" triangle.
These started out as leased cars, with marking GAEX. This was a joint venture between General American and Evans equipment. Once the lease was out PRR purchased a large number of them, and then GAEX was dissolved. There is evidence of some of the PRR cars lasted into PC days.
These GAEX cars can also be seen with other railroad markings such as B&O, GM&O, UP, C&NW, etc. I am unsure if the railroads purchased them, and then put there own marking on it - of if the having the leased railroad painted on the car was a 'feature' of the GAEX leasing agreement.
Boxcar Roof Walks
A quick note about Roof walks. I know that the roof walks are no longer seen on modern boxcars, but I had not known the specific dates for this changeover. While listen to Roy on his "N-Scale Union Pacific Evanston Subvision" youtube channel, I learn that:
"In 1966 the federal government announced that boxcars ordered or delivered after April of that year would be built without roof walks. And that roof walks would have to removed from existing boxcars by 1978. Although this date was extended to 1983"