Lets have a list of the crimes of Kefka, Sephiroth, and Kuja:

Kefka:
- Attempts to burn down two areas: Figaro Castle (fails only because they then go under ground) and Thamsasa (arguably, we don't know if he succeeds or not, but it doesn't really matter after the WoR occurs)
- Poisons an entire Kingdom, killing all inhabitants except one
-Unleashes three bound gods, uses their power to blast his emperor into submission before jumping on his neck to break it and kicking his corpse over the side of the Floating Continent
- Kills his fellow general after he corners him for attempting to carry out the destruction of Thamsasa
- Destroys the Esper's land and proceeds to basically carry out a mass genocide against them, turning them into Magicite
- Becomes God and decides to destroy the world bit by bit, reveling in the despair and misery of the people instead of destroying it outright; technically had achieved complete victory for a year before being defeated.

Kuja:
- Controls and manipulates an entire kingdom, starting a near world-spanning war
- Kills his own mentor
- Goes trance and proceeds to destroy HIS own entire homeworld
- Damages the life sustaining crystal in an attempt to brind death upon all things, thus releasing Necron

Sephiroth:
- Burns down a village (is cut down shortly thereafter by Cloud and remains a corpse enclosed in ice for five or so years)
- Kills the Midgar Zolom (not a real crime; merely killing a monster and impaling it isn't exactly against the law)
- Kills President ShinRa and several ShinRa employees/soldiers (the employees can somewhat be considered innocents, but it's hard to feel sorry for ShinRa and the soldiers)
- Kills Aeris (thus sealing his own failure)
- Summons Meteor (arguably the only thing he had really succeeded in doing truly right)

Sephiroth was an interesting character to an extent, but in terms of pure evil and maliciousness, Kefka and Kuja EASILY trump him.