None of the above. Feeblemind is a unique spell effect. It is somewhat similar to a penalty or Ability Drain, but it is not the same thing. The victim's Intelligence and Charisma both "drop to 1", regardless of their normal values. This is neither damage, nor penalty, nor drain.
It's definitely not Ability damage, because damage doesn't actually change the value of your ability score. Ability damage is a temporary reduction that can be restored naturally. Ability damage is automatically healed by 1 per day, and can also be healed by spells like Lesser Restoration. Also, Ability Damage to Intelligence doesn't cause the victim to lose skill points.
The effect also is not a penalty, for similar reasons; penalties reduce the score by a specific amount, penalties have a limited duration, and penalties have the same effects as Ability damage.
You could compare Feeblemind's effects to those of Ability Drain, because the consequences are similar; that is, Intelligence and Charisma are reduced, potentially forever. Ability drain has a permanent decrease on the ability score, and all related statistics get recalculated accordingly:
Ability drain actually reduces the relevant ability score. Modify all skills and statistics related to that ability. This might cause you to lose skill points, hit points, and other bonuses.
Feeblemind similarly reduces the ability score, and so it would also cause a loss of skill points. However, Ability Drain can be healed through spells like Restoration, whereas Feeblemind cannot; only Heal, Limited Wish, Miracle, or Wish can remove it. Therefore, they are not the same effect, but have similar consequences on skill points. Note that a generous GM could hand-wave the loss of skill points for simplicity's sake, especially if the spell activates during combat.