The opportune parry is treated "as if she were making an attack of opportunity"; it seems like if you can't take an AoO against the incoming attack (say, because it's incorporeal) then you can't parry it. It also appears to be in line with RAI at least to add a miss chance if the swashbuckler is using a magical, but not ghost touch, weapon to parry an incorporeal attack. (In previous editions, the miss chance would have been RAW, too...)
Likewise, a swashbuckler should not be permitted to parry attacks by invisible creatures, attacks from creatures he is unaware of, any attack while flatfooted (without the Combat Reflexes feat or similar), or any other attack where he couldn't AoO the attacking creature or its weapon. (As a side note, the only two times I can think of where "the attacking creature or its weapon" should give different results for the creature and the weapon is in the case of reach weapons, where the weapon comes into the swashbuckler's reach despite the wielder staying safely away, and the case of a ghost touch weapon being used by an incorporeal creature, so the swashbuckler can swat the weapon away but not touch the wielder.)