It mostly depends on the talent in question and how long the cooldown is. Most of the time, you're probably better off using the shorter cooldown first because most fights don't last that long, and you have a higher chance of using a short cooldown twice. If one talent is significantly better than the other, it may be worth using that one first just to swing the fight in your favor right away.
Only major boss fights are likely to let you use a single talent with long cooldown more than once.
Okay lemme give an example. Say I have two 16 cooldown shield runes and the skeleton racial generic talent bone shield (Cooldown 30), as well as arcane reconstruction (Cooldown 15), healing light (cooldown 10), and the skeleton's healing talent (41-25). In what order should I use these when I need healing and shielding?