The final battle of Final Fantasy VI. It definitely left an impression on little old me, even if I didn't understand the allusions when I was a kid...

Otherwise:

FFI- Chaos
FFII- Emperor battle
FFIII- Zande battle
FFIV- Four Fiends battle, Zeromus battle
FFV- Gilgamesh battle (s), all X-Death/Exodus battles.
FFVI- Final battle, battle with Ultros during the opera.
FFVII-All Jenova battles. Final battle.
FFVIII- Wacky Time Compression Sorceresses.
FFIX- 'You're Not Alone' battle in Pandaemonium.
FFX- Battle during the Bevelle wedding, battle with Sin, final set of battles
FFT- Final set of battles, anything with Delita-witten.
FFTA- Remedi. Enough said.