FF IV - Demon Wall
FF V - Gilgamesh in Exdeath's castle
FF VI - The battle against Vargas that introduces Sabin and his Blitz... but for all the wrong reasons >_> positive side would be Ultros 1.
FF VII - Carry Armor, mainly due to this.
FF VIII - The Oil guys on the Garden's MD level. They're actually pretty threatening.
FF IX - Hilgigars, also for all the wrong reasons. More positively, Black Waltz 1.
FF X - Yunalesca for sure.
FF X-2 - I'll count the Den of Woe gauntlet as being the main villain, so instead gonna say Bahamut.
FF XII - Probably the Mimic Queen.
FF XIII - The second time you fight the scorpion dude, because I kept dying instantly at first since I thought I was smart in not putting a Sentinel tank on my team since they seemed pretty superfluous. Little did I know having one is near mandatory for the group damage reduction, otherwise the ice attack instakills you. Other than that, Odin and Hecatoncheir, are both high candidates.
FF XIII-2 - Proto-Fal'Cie Adam