The people who build aftermarket intakes live and die by the peak horsepower numbers. I can't stand peak HP engines because they suck to drive anywhere but onto a dyno. Also, shorter intake runners are easier to fabricate and they package better.
Since I'm going forced induction with a (relatively) big turbo, I'm building the intake for torque and letting the turbo take over up top. A good place to start if you are running the stock cam is to just make them the same length or a little shorter than the stock runners.
Here's another good explanation.
http://www.team-integra.net/forum/blo ... er-size-calculations.html