Builders: Square engine, Over Square, or Under Square for you?

Over square every time.

The quote below is from Darin Morgan;

"An oversquare motor is absolutely superior at high rpm compared to a long-stroke motor of the same displacement. Formula One and IRL motors are hyper-oversquare, meaning the bore is twice the size of the stroke. If I could do that in a Pro Stock motor, I'd do it overnight, and the power would go up accordingly.
Once piston speed hits a certain range, frictional power losses sky-rocket. By decreasing stroke and increasing bore, you're not only dragging the rings up and down the bore that much less, but you also have less windage, the crank counter-weights get smaller, rod angularity decreases, deck heights get shorter, and the induction system package looks a lot better.
With a bigger bore and a shorter stroke in a high-end engine, you don't need a tall-deck block. That lets you move the valve-train closer to the deck, shorten the pushrods, reduce the resonance frequency of the pushrods, and wind the motor higher with less valvetrain flex.
In a high-end engine, you always use the biggest bore and shortest stroke you can get. However, there are some exceptions to the rule and you have to look at the entire engine package as a complete system."
Without reading all this thread, I feel you can drop the mic right here and be done/right.