Most circuits use a 2N3055 power transistor to drive an ignition coil. A Google of "Ignition Coil Circuits" will bring up a collection of circuits like this one. Three terminals is normal as you have a common ground connection on the coil. If the fence is metal and grounded the no, you can just connect the HV output to the metal. Electrified fences normally have stand off insulators with the high voltage wire isolated from ground. You can't electrify a metal fence that is grounded.
Usually you would have the entire circuit grounded to a metal stake pounded into the earth. The high voltage output is normally a high voltage with respect to the ground of the circuit, so the HV output on a wire fence should work to keep animals (who are touching the ground) away from it. As Ron mentioned, though, it really depends on the type of fence. If you just have some posts in the ground and wire strung between them (with standoffs), you should be fine. If you have a chain link fence, however, that is built into the ground, it will not work. It will simply create a dead short.
I've seen in many ignition coil driving circuits they used the free wheeling diode across GND & collector of the transistor.Not across the ignition coil.
Whats the reason to this?
Also for snubber they don't use a resistor, just placing a capacitor across the transistor???Those stuff are never to me.