FFI: Garland/Chaos, Elemental Fiends: Lich-Marilith-Kraken-Tiamat, Chronodia
FFII: Emperor Mateus, Astaroth (harpy), Beelzebub (crazy fly), Arena Behemoth, Borgen/Zombie-Borgen
FFIII: Cloud of Darkness, Hecatoncheir, Garuda(Bird-man boss), Goldor, Hein/Hyne, Doga & Unei, Xande
FFIV: Giant of Babil, Zeromus, Elemental Archfiends: Scarmiglione-Rubicante-Cagnazzo-Barbariccia/Valvalis, Dr. Lugae, Demon Wall
FFV: Exdeath, Abductor (Imp), Archeoavis, Azulmagia (Corse), Byblos (Demon), Catastrophe (eye), Galura (Marid), Halycanos (demon), Mellusion, MoogleEater (Kraken), Necrophobia (Vampyr), Liquid Flame, Gilgamesh (2-arm & 6-arm), Gogo, Omnicient (Soulflayer?), Sol Cannon, Twintania (FFV had a lot of bosses of note...)
FFVI: Kefka, Warring Triad, Ultros (Kraken), Whelk (Urganite), Hidon (mutant taurus?), Air Force, Atma Weapon (bio-engineered behemoth), Chupon, Vargas, Ziegfried, Siegfried, Chadarnook (similar to Mellusion), Dullahan (chariot), Inferno (Iron Giant), Magi Master, Phunbaba
FFVII: Sephiroth, Ruby/Emerald/Diamond/Ultimate WEAPON, Proud Clod (maybe Minerva), Midgar Zolom (worm or amphiptere), Gi Tribe (demons/taurus), Materia Keeper (scorpion)
FFVIII: Ultimecia, Adel, Edea, Griever (Khimaira), Norg, X-ATM092
FFIX: Kuja, Ark, Garland, Necron, Ozma, Black Waltz (group), Gizamaluke, Thorn/Zorn (Automatons?) combine to form Meltigemini (Mumbo Jumbo) Hades
FFX: Yu Yevon, Yunalesca, Braska's Final Aeon, Seymour Omnis, Chocobo Eater
FFT: Elidibus, The Lucavi: Wiegraf/Velius-Adrammelech-Belias-Hashmal-Cuchulainn-Zalera-Altima, Delita, Celia & Lede
FFXII: The Undying, The Judges: Drace-Gabranth-Zargabaath-Bergan-Ghis, Vinuskar, Yiazmat (maybe a boss that the entire server can try to take down over a period of weeks - HP never regens.)
I'm sure there are other bosses that would make interesting enemies in FFXI (although, these, and some like them could appear in FFXI as actual story-related characters, or NMs and BCNM enemies, also Summons and other recurring characters, rather than appearing in this arena, although, having a retro version in the arena would still be fun.)