For D&D, I prefer numbers for weapon damage, energy damage on a weapon, etc., but pips for sneak attacks or nukes. IOW, if it's a few dice, numbers to match the rest of the dice set; if it's a lot of dice (which includes d6 systems), time to pull out the box-o'-d6.
I used to be pro numbers, but I've since gotten to many cool sets of piped d6s I've changed my views. Plus I like minid6 and for the most part they only come in pip form.
Numbers, simply for aesthetic reasons. All my other dice sizes are numbered rather than pipped, so you get a uniform appearance if the d6's are numbered as well.