Hardness.
While incorporeal, you can only pass through objects with hardness less than your rank of incorporeal. Apply to attacks by giving attacks a 'hardness' rating equal to their damage bonus. Attacks can affect you if their rank meets or exceeds your incorporeal level. If they are below, they pass through, with the exception of the one type of attack you are susceptible to. So a fellow that can do +12 damage on an attack forces you to make a damage save of 15+12-(incorporeal rank).
Not a perfect system, but it prevents players from cheesing out with incorporeal to become immune to damage, while still providing the benefits of being incorporeal. If they want the safety incorporeal provides, max it out.
In addition, if you have the ghost touch extra, your extra rank (or incorporeal rank if not using partial extras) is the maximum bonus to any form of action using ghost touch. Energy blast using ghost touch of +1, but you have +8 energy blast? You get +1 energy blast. Punching with a +6 damage bonus but ghost touch of +1, you get a +1 damage bonus.
So many people want to use incorporeal, that I always look at it and wonder how I can use it 'safely' in my game. In EPIC, incorporeal only gives you the ability to move through objects and ignore unpowered physical melee and projectile attacks. Otherwise, I use the rules above. Mind you, only NPC's currently have this power, and nobody has attacked them in that form yet, so I've yet to test it out fully.