I know animal tracking has been suggested but it relates to my suggestion of improvements to the Stealth skill so I decided to clump them together.
As many people know Stealth currently is useless as a ranger can just enter and exit a building to see the scents. This system needs a change so that is a worth will skill to raise but I am suggesting another use for it...
Area of Agro
Stealth should affect an animals ability to initiate combat with you, the greater your stealth the less likely it is for the animal to see , and attack you. If some one is hunting they might like the animals to naturally agro to them and so there should be a "Stealth Mode" toggle. When toggled off, the system is like how it currently is, stealth not mattering. When toggled on it is like how I suggested, where stealth decides the range of the animal being able to see you.
A possible formula for this would be
animals sight/sqrt(stealth*int)*10(or however many tiles the base detection is now)
Also, having Stealth Mode toggled on should never negatively affect you. For example if having it toggled off means animals can see you within a 20 tile radius, then having it toggled on would mean that if solving the formula resulted in anything greater then 20, they'd still only be able to see you within the 20 tile radius.
Fleeing
Your stealth should also affect your ability to flee from combat with anything, animal or person.
Your stealth as compared to an animals sight number or a persons perception*exploration (although this would add another use for perception and exploration, and they are already quite useful as it is) would affect how many tiles you have to move away before it'll disengage you from combat.
A possible equation for this could be:
sqrt(perception*exploration of the one not fleeing)/Sqrt(stealth*intelligence of the one fleeing)*20
To initiate the fleeing mode you would have to right click that two swords next to the portrait of the attacker, that way having high stealth can never cause a fleeing animal to have an easier time getting away.
Tracking of Fleeing Animals
The mechanic of animals fleeing should be the same as the when people flee. When fleeing, animals should also run at one speed slower then normal because an injured animal wouldn't run as fast as perfectly health animal. If combat is disengaged when the animal it should leave a scent, either immediately in the persons inventory, or at where the animal was before it fled. The ability to see the scent should be determined like the ability to see any other scent (with animals having a pre-determined stealth and int) and since most of the times animals are not near any houses or anything, the normal entering and exiting of houses won't work for seeing the scent.
If you kill a disengaged animal by tracking the scent (left click to pick up scent and right click on the animal to engage combat with it again) you will get a percentage of the LP lost by it disengaging from you.
Thats all I can think of for now, I'm sure I missed a few points but I will edit if any of them come back to me.