I tend to think of red lights as a warning, so most of the time I reserve red LEDs for things like over voltage indicators — of which there aren’t many. Mostly I use green. I never thought about different colors for different modules or types of signals, but if I had, I don’t think I would’ve done so.
When I built the Haraldswerk sequencer I used blue LEDs just because I didn’t like green with the purple knobs I’d chosen.
We’ve disputed red/green bicolor LEDs before: Some like red to mean positive, as in red insulation for +V, while I think of LEDs as analogous not to wire colors but to traffic lights, hence green for positive (accelerate) and red for negative (decelerate).