ORIGINAL: Rodney
Brownknows, it makes no difference which way the grain goes as the stress is at a 45 degree angle to the span and switches 90 degrees as you change from positive G's to negative G's. If you don't believe this just check out any strength and materials book on beam design. It is usually easier to put them in with the grain vertical and will work just fine in that manner and is a good compromise; however if the grain ran spanwise they will be just as strong when it comes to resisting G loads.
From a structural engineering point of view I don't know which way is best, However, That being said I can speak from some 1st hand experience. I acquired a used Hobbico superstar (pre Monokote) which had loose sagging covering. Over the winter I decided to recover it. After removing the old covering I noticed that on both ends of the wing the shear webs were split on the inner 3 or 4 bays. You guessed it, the grain ran parallel to the spars. There was no obvious signs of a crash which required any repair so I assume that it had lived an easy life up to that point.
I have always placed the shear web grain perpendicular to the spars and will continue to do so.