Kefka is the best villain overall. Great design, one of the greatest boss fights and themes ever. In a lot of ways he basically established a lot of the things the villains after him would just ape and copy over and over again, but do worse. Most of his motives and plans were understandable given his situation too. He is a somewhat tragic character that ultimately works well with the clown/jester motif as, in the end of the day, he truly was someone who was experimented on so much he had lost his sanity. Treating people beneath you is fair when you are given a role of power and cannot relate to others. Wanting to rule the world makes sense when suddenly becoming the most powerful being in existence. Wanting to destroy the world also makes sense when realizing that there is no joy or happiness to be found in ruling the world, and that the only people that seem to be able to feel love and happiness are the ones you feel are too beneath you to bother with. It is so much better than the motives of characters like Sephiroth or Ultimecia or ironically my second pick...

Kuja. I think he is extremely memorable because 9 ultimately is supposed to be like a child's fantasy book. He is a petty cocky horrible person that always thought he was above others and in control. Once he finds out his life is finite and ending soon, he lashes out on the world. That is honestly a great motive for this kind of story. But what really seals the deal for me and makes him so memorable is that in the end of the day, he chooses to use the last of his power to save Zidane and the party instead of trying to prevent them from escaping. That is his final act in life. Death was the thing he feared the most, and he chose to save others as he faced death. That single action completely changed the way I looked at him and turned him from being forgettable to one of the best JRPG villains to me.