FF7 and the Underwater Materia. Its Aire Tam attack was instant death.
Even the Ruby Materia was a pain.
You mean the Emerald and Ruby Weapons.
Aire Tam (Materia spelled backwards) Storm does damage directly proportional to how many Materia you have equipped.
As for Ruby, start the battle with a single character alive and have them use Phoenix at the start of the battle.
I'm not sure what the most annoying attack I've encountered would be, but a thief in Disgaea 2 would be the cheapest by far (guaranteed to hit sleep/ poison attacks means a naked level 20 thief can kill a level 9999 Divine Majin).