Final Fantasy IX is unique compared to other games in the Final Fantasy series in that there are no explicit “Ultimate Weapons” for all of the characters. Below is a list of what are arguably the best weapons for each of the characters and where to find them:
The most powerful weapon for Zidane is the Ultima Weapon. You can find it by using a Dead Pepper near the fourth Dive Spot near the Shimmering Island which is part of the Chocobo Dive Spot side quest. The fourth and final dive spot can only be reached on Disc 4 of the game.
Ultima Weapon has 100 attack power and teaches the Flee abilities and can inflict the Sleep status effect.
Mace of Zeus teaches Vivi his most powerful spell: Doomsday. It can also teach the inflict the Mini status effect.
Steiner has two Ultimate Weapons although one of them is extremely difficult to get. The Excalibur II is not only the most powerful weapon for Steiner, it is the most powerful weapon in the game. The weapon can only be obtained by completed the Excalibur II side quest which involves reaching the end of Memoria in under 12 hours - arguably one of the most difficult side quests ever created amongst all Final Fantasy titles.
Excalibur II teaches Steiner the Minus Strike, Climhazzard and Stock Break abilities and has 108 attack power.
Because of the difficulty of obtaining Excalibur II (which you basically have to spent the full game speeding through just to obtain it) the second best weapon for Steiner is normally considered is Ultimate Weapon. It is the Ragnarok and it can be obtained by locating Chocograph #21: Outer Island through the Chocograph side quest.
Freya’s Ultimate Weapon is called the Dragon’s Hair lance. It can be obtained by opening the third Chocobo Mountain Crack by using a Dead Pepper while standing in front of it. Check out the Chocobo Mountain Crack side quest page for more information.
Dragon’s Hair can teach Freya the Dragon Breath abilities which deals a good amount of damage to enemies (Target’s max HP minus the current HP, thereby doing more damage later on in a fight).
The Gastro Fork can teach Quina the High Tide ability and can inflict the Stop status effect.
Eiko’s Ultimate Weapon is called the Angel Flute. It can be found in Memoria in the “Past” room (which is the one that has the Save Point up on the pedestal). There is no treasure chest - the Flute can be found by searching the area and pressing the Button repeatedly.
The Rune Claws are Amarant’s Ultimate Weapon. They can be found in Memoria as well in the “Time Interval” room which is the one with the stairs leading up to the giant eye (the Invincible ship). Search the area off to the left of the stairs to find them.
The Rune Claws will teach Amarant the Spare Change, Demi Shock and Revive abilities. It can also inflict the Darkness status effect.