Really this is just sort of a thread for my miscellaneous home rules.
1) I use optional collisions (not immediately lethal). From The Rules of Air Combat.
2) I use the optional bailout rules form wings of honor. This means that if a pilot fails a bailout roll, he does not immediately die, but instead takes 1 point of Constitution damage for every point he failed the roll by. Tends to keep your pilots safer.
3) Kills. I use the rules for half kills in Rules of Air Combat. However, regarding noncombat bailouts - If the plane will be defeated (such as a burning magnesium round or drill rocket heading for the pilot/fuel tank/engine/about to saw off wing) then the pilot who bails out loses no experience points, and the person who inflicted the damage gains a full kill.
4) Healing. If a pilot loses Constitution from battle wounds, then it heals at a rate of 1 point for every mission the pilot sits out. So if your wingman took one point of damage, and sat out the next mission, he would be back to normal by the misison after. This requires both a trained medic and sufficient medical supplies. However, serious wounds (pilot's normal Constitution divided by 3) then the wound is too serious and may not heal, it must be improved using experience points. Note that this only applies to pilots of Constitution 5 or higher