I use them for a couple things depending on my mood and how I am playing the game. When I am playing fast paced not bothering to name creatures just playing to play with no attachment to the nichelings I use them to mark "disabilities". This meaning,, I identify the three worst traits in my tribe at that moment and I give each creature that has on of those traits a red gem for each one. If a creature has one or no red gems they can breed and if they have two or more red gems they cannot unless absolutely necessary. Once my nichelings reach a point where their genes are no longer heavily affected by the original three I reset gems back to green and pick three more genes I do not want and remark creatures according to what genes they have proceeding with the 1 or less can breed 2 or more cannot.
When I am playing with attachment to my creatures/building a small story around them I use colors to mark breeding pairs leaving one color for the non breeders. This allows me to remember their "mates" and reminds me of who has genes I don't want...It makes for less straightforward genetics, but it's nice to have dedicated couples in the game sometimes.