Skullbriar and Phyrexian Ingester
Sorry, my previous response was incorrect. We apply the Ingester's ability in layer 7c, but we don't apply effects from counters until layer 7d. At the point when we're determining the bonus for the Ingester, we haven't gotten to the point of applying bonuses from counters. No matter how many +1/+1 counters are on Skullbriar, at the point we need to figure out the bonus for the Ingester, Skullbriar is a 1/1 creature, so the Ingester will only get +1/+1 from Skullbriar, not +3/+3, making the Ingester a 4/4 creature.
Nathan Long
Magic Rules NetRep