I train both, probably around 50/50 and compete raw.
I found I like free squats better b/c they feel much more natural. Box squats, done properly, load the glutes and hams more than my free squat, but I think they undertrain the hip flexors and outer quads (the muscle that gets stretched in the hole b/c it crosses the hip). At least that's what I feel in comparing muscle fatigue and soreness b/t the two.
I think there's good carryover but I suspect this is highly personal (form dependent). I squat wide and my box squat stance is only slightly wider than my free squat stance.
I also think that training box properly with your butt way back and keeping your shins vertical helps preserve your knees over the long haul b/c of decreased loading on the joint.