Omega Weapon's Medigo Flame deals, as rubah noted, 9998 damage to all characters. While full health and 9999 max HP can circumvent this attack, it's also possible to have a GF "block" it by taking the damage for the character during the summoning process.Originally Posted by Tensa Zangetsu
Omega Weapon also has Light Pillar, which has the same effect as when Ultima Weapon uses it. One target will take 9999 damage.
Once you've used Phoenix in battle, it will sometimes appear during random battles and perform Rebirth Flame, reviving KO'ed characters, which can save the party from annihilation. This is the closest FFVIII comes to having an Auto-Life type spell.
And, yes, invincibility items guard against anything, although Omega's predictability removes most of the difficulty from the battle. They're really not necessary.