A really good strategy/ civilization game?

Could you be thinking of “Transport Tycoon” by Chris Sawyer? You built not only railroads, but highway/road systems, harbors, and airports, along with buying trucks, boats and planes. I used to spend entire nights designing and building entire transportation systems.

ETA forgot about the water shipping

Ahem. Try “Xplorers” here.

The original Black and White might fit your criteria.