List so far contains:
-> more experience gained during PvP battles
-> when in a nebula: secret base production and interest is stopped
-> PvP planet combat salvage from Raids, Conquer attempts
-> Increase salvage rate on PvP attacks when enemy ships are destroyed
-> Total annihilation of the enemy fleets bonus, special item e.g. turn item or CP when the attacker kills 100% enemy fleets. Power of the item(s) depends on the enemy fleet power.
Some of these suggestions sound like they could lead to abuse by Friendly Fire (PvP against an ally, like cam mentioned)
The nebula solution is not the greatest. If there is a penalty for a nebula then one only needs to reserve all fleets before logging off (which is what many top players do and is even more anti-PvP than nebula protection) and they will continue to get their mining facility / planet production income.
I am someone who (although I have NEVER been buddy nebbed), uses pships to save money on not having to buy marines. For me, an incentive to stop doing this would be to make it impossible for a commander with 100x my wealth to want to attack me (he really has nothing to gain from it anyway, he only does it because he can, and has nothing better to do). If I don't have to worry about attacks from those commanders then I can start looking for targets in my range.