Ultros #3 and Ultros #4 cannot be joker doomed because their formations are specifically exempted by the joker doom code. Dullahan and the Tentacles cannot be joker doomed because neither Setzer nor Gogo can be present. The three tiers in the battle are also immune to joker doom but a 7-7-Bar can be redirected back at them.
FlameEater, Poltrgeist, Inferno, Guardian, Air Force, and the Tentacles are immune to Vanish. :) Neither JD nor VD solve every problem!
Wandering Road is right about the boss battles staying interesting. Using the proverbial Bane Sword is dissapointing but it is at least 100x more interesting than watching Magus swing his scythe for 5 minutes. The bosses in Kefka's Tower have approximately 40,000 or 60,000 HP each. Yeah, I could smack 'em six times with a lvl 6 zombie-drainer for 9999 (I just learned about that glitch yesterday) and then let Kutan punch 'em for 6 damage but that would take a long time to setup and execute. For example, Mog needs Tapir for that trick to work. Don't get me wrong though - having a lvl 6 character do 9999 is awesome and a killing blow of 6 damage is priceless. But after watching deperation moves for 2 hours I think ID is the way to go.