On an absolute scale, any of the weapons from FFX is the most powerful, because you can do 99999. The weapons don't really even matter, because your damage is mostly based on Strength anyway.

On a relative scale, Illumina and Ragnarok (both from FF6) are probably both the most powerful. Illumina gives better stat bonuses and randomly casts Pearl, but Ragnarok randomly casts Flare, which is a better spell in my opinion. That has the potential to equal 19998 damage, which is twice the limit (9999 for the actual hit plus 9999 for the spell).