Once upon a time I though holes and cutting away sections was best, so my dyno graph said.
Then I cut away a little bit more, and my power was down.
After research and more research, and speaking to some people (people who actually know), I came to the conclusion that a sealed airbox, with the inside smoothed and the intake pipe on the inside rounded off and one or two sealed cold air intakes, giving the airbox more air than it's using, is the best method. It might not sound as loud as a drilled airbox but performance-wise it's the best setup.