Wanderer, it sounds like you're like me, coming from a background of house wiring - 120 and 240 V AC. As a building contractor for many years, the convention of black and red for hot, and white for neutral, was so drilled into my head that it was unquestioned - which is as it should be, in that context. House wiring would never pass building inspection, and would be downright dangerous, if every electrician made up his own idea which color wire to use for hot.
But I learned pretty quickly that is not the case with low voltage hobby wiring. As you note, a lot of 2-conductor low voltage wire comes red and black. So using white as neutral was not an option, brainwashing or not. So I just settled on my own standard, and stuck to it. Black is neutral on my layout.
And I found that most of the 4-conductor I bought was red, black, yellow, and green. Since a lot of signals and turnouts on a layout show red and green lights, it makes sense to use the red and green wires for them, keeping black as common and then you are using the yellow as your line hot.
Sometimes you end up with good, useable pieces of wire that are the "wrong" color. In house wiring this is not an option, but in hobby wiring it can be more economical to use these instead of cutting into a new roll. Just try to be consistent, and as Dale notes, you can mark the ends of odd-colored wire with colored tape to conform to your own "code".
david