Sounds like a cool idea, a few questions and comments :-)

Have you thought about the graphics side of it? I was just sitting here thinking on how it would look from a isometric or top-down view of a game like that, since I found 3D could make thinges difficult (atleast in my head).

Another animal for your farm:
Horses, only affected by the people.

Things that might make the levels harder later on, like:
- Wolves: chases/scares the smaller animals like pigs and sheep
- Bears: chases/scares everything

Issues...
1. What happens if a herd of animals gets to a juntion witrh more than one exit. (I think depends on animals type - sheep/goats go only one way, Cows/Pigs split into two groups). Could this be used as a strategy to accelerate results?
I guess that'll depend on the size of the herd, and the speed (i.e. if they are just walking it's easier to follow than if they are running from something that scares them). Also if one of the junctions are narrow and it gets crowded, the rest might just turn to the other one since there is free space.

2. What negative effect do various tools have. A noisy moving tractor may scare the cows, the barking dog may panic the sheep.
There is another aspect, because, they can end up getting used to noisy things as they grow older. Some goats in the real world don't even move if you use the carhorn on them, so they get used to anything. But the offspring (or whatever it's called) of all these animals might be running away as soon as something makes noise :-)

3. Scoring, possibly timed levels, possibly other goals.
reduction in points if some of the animals walks of a cliff, or gets nailed by nasty animals.

Would be nice to see one of the maps just to see how it looks like in your head. For all I know I could be far off on this one, but it's atleast my 2 cents :-)
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Eriken