Im installing a cold air intake and have seen some people use the line from the intake to the breather just below the oil fill cap, and have seen some people use just a small air filter on the crankcase breather, and plug the hole on the air intake for the hose. What would the differences be?

 

Vents to atmosphere vs venting to intake and recycled like the factory does it.

 

That tube isn't a vent, it's an intake, it pulls fresh air from the airbox/filter and draws it into the engine through the oil fill tube. It exits the crankcase at the intake manifold via the PCV valve. Bad PCV valves will allow vapours and moisture to blow back into the intake area making it look like that's where it vents.

The difference in using the tube basically boils down to pulling air from the engine bay or from the airbox.