I think Sharris has the right answer: one resistor for each LED.
True, you can manage with one resistor per head, but you cannot adjust the relative brightness of each LED that way. I think it would be a good plan to find out the correct (or suitable) resistor values like sharris suggests for each colour of a LED and this way match the brightness of the LEDs, and then (with power switched off) measure the common resistance over the combined 1k fixed and adujustable resistor for each LED colour, and use those values when purchasing the resistors for each colour of LEDs. Resistors are cheap.
I would also suggest taking the common wire of each signal mast or gantry through a rectifying diode. Any cheap small rectifying diode will do, like 1N4148 or 1N4001 or similar.
Why?
The diode would protect the LEDs aginst accidental polarity swap, as the LEDs will not generally tolerate reverse voltages in excess of 5 volts or so. If the supply voltage is accidentally reversed, the series resistors will not reduce the voltage seen by the LED, as no current will initially flow, thus the resistor will not create voltage drop.
I'd put the resistors and the diode close to signal masts (gantries), right to the ends of the thin drop wires and cover the soldered joints with heat shrink tubing like sharris suggests. When the signal mast or gantry is removed for repair, painting or whatnot the resistors and the diode will come out with the signal mast (or gantry), and when checking the signal mast at the desk one will not accidentally apply full voltage directly to the LED. If one is fiddling with the wiring within the control panel or cables and connectors between the layout and panel, the accidental shorts or power reversals would not distroy the LEDs as the resistors and the diode are near the LEDs they are to protect.
I have once in my youth exploded a (then rather expensive) LED due to applying reverse 9 volts from a battery directly across LED terminals -- good thing I had my glasses on.
pekka