What do the skulls mean in shadow of Mordor

Solution 1:

The White Skull can be considered the generic one because it just indicates that the Uruk in question is a Captain

The Blue Skull is a Branded Uruk Captain, branded by you ofcourse.

In Battle you can have Yellow Skulls and Green Skulls. Yellow is when you are detected and that Uruk captain is investigating and Green is when he can be finished off in battle.

There is a variety of all the Skulls with a Red indicator, as you can see here:

In the picture you can see a White Skull with the indicator but it can be any type of skull.

Solution 2:

No, the skulls don't turn yellow and red based on how alert they are to you. Those are the triangles over enemies' heads. A Gold skull means it's a captain that's also a quest objective. A Green Skull means the captain is weak and can be grabbed.