no FF boss is hard if you grind like crazy before facing. I recall killing Ruby weapon with Knights of the round on W-Summon, and then mimed by the other 2 characters. I want to say I got 6 straight KOTR each hit doing 9999, and yes he died. But it took me forever to lvl up Master my W-Summon and then master Mine and then lvl up the 2nd mime (game only gave you 1 mime so to get a 2nd you had to master the 1st)

It wasn't the hardest technically, but that fish boss from Majora's Mask came at a period of time where I was terrified of sharks, so swimming down and waiting for him was super scary and made it hard in that sense.

There are five, though the Brohannes are actually kind of easy, but so is Astrodotus, but the other three are nightmarishly difficult. 

I'd also add Ozma from ffix, even if you go through all the steps to make him more vulnerable you're still going to need some luck to beat the bastard.

I have never managed to beat Kintaro from Mortal Kombat 2. I will fire it up on my SNES soon and give it another go.

Could be Lingering Will/Terra Armor in KH2 fm on critical mode

Catherine Final boss at hard was really challenging.

Pixeljunk

https://www.youtube.com/watch?v=giYGo7ndjnQ

This one made me rage so hard. I just couldn't do it ;(