An exceptionally made piece of Armor will gain a 15% bonus that is distributed randomly among the base resistances of that item. For example, an exceptionally made Platemail Tunic could have 5% applied to Physical, 6% to Fire, and 2% to each Cold and Poison. Or, and this would be extremely rare, all 15% could be added to Physical.
Exceptionally crafted armor also receives an additional 1% bonus (again randomly distributed) for every 20 points of Arms Lore your character has. The maximum bonus is therefore 20%. However, the total additional points from Exceptional and Arms Lore is capped at 20%.
Charged items (such as Tools) will have more uses attached to them if crafted exceptionally. Items such as furniture receive no benefits other then the Maker's Mark. Musical instruments gain an additional 10% likelihood to affect monsters.