I actually acquired 2 RS-3s at a recent auction but haven't received them yet. Were they used for freight trains? They kinda looked like big, glorified switchers to me, but I know nothing.
The RS-3 was sold as a "Jack of all Trades" kind of locomotive. They were used in switching service, freight service, and passenger service if equipped properly. Most spent their days in freight service. One of my favorite photos of the RS-3 is during the Penn Central era where a GG1 is leading three RS-3s on a long freight train. Just an interesting mix of power.
As to smaller diesels in general service today, the RS-3 is not very common. Most saw their last miles in the 1970's. Alco power in general just isn't that common on today's railroads. A few still operate for short-lines and tourist service.
Most diesel locomotives in service today for freight service would be EMD or GE power. What constitutes a switcher anymore is anyone's guess. One can find EMD SD40-2s doing yard duty while MP15 (the modern equivalent of an SW unit) can be found pulling mainline trains. The good news for us as modelers is that it really doesn't matter what we use for mainline operations as long as we enjoy it.
Like others have said, GP units would be a great start if you are looking for prototypical realism. GP38's and GP40's are still very common in service after a few rebuilds. They have a fairly short wheelbase. More modern wide cab GP60s are also a possibility.
Once you get to the short-line roads though nearly anything goes including former passenger locomotives from the F7 to the F40PH. Maybe not 500-mile-long roads, but certainly interesting operations.