It would be very helpful to be able to assign different colours to guidelines. When clicking a guideline the context menu already shows the colours available, but they don’t change the colour.
(I know there was some comment about using alignment zones as visual guides, but when working on complex non-Latins there can be many, many different alignments, more than the seven (?) alignment zones allowed by OpenType.)
Six top zones, five bottom zones. But you can have as many as you like inside Glyphs.
Ah, ok, but that doesn’t solve the problem of them all looking the same colour 
(And those alignment zones would need to be manually removed before every export…‘too many alignment zones’ error otherwise.)
I think that your problem is better solved with a Reporter Plugin and custom parameters. How many different colors would you need?