"That's good Snake."  "Hurt me MOOOOREE."

the fist fight with gray fox in MGS1.

The other would have to be the mantis ant in secret of mana.  It was the beginning of the end for me.

Zophar from LUNAR 2.  Not a great villain really, the villain from the first LUNAR is actually far far better.  But the four-part epic fight itself it great, and the music is fantastic.

Majora's Final form definitely fucked me up for a while, especially since I didn't have fierce diety's mask, nor do I want to use it.

I found Majora to be a more challenging, and memorable boss fight in comparison to Ganon. 
Great music, great use of strategy, great AI.  Majora was a fun fight.

The whole section leading up to this bossfight was just so surreal, unlike what any zelda can/has offered as of late.  Majora's mask was really different and that's probably why I liked it more than ocarina of time.  The Fight with Majora consisted of a relentless changing AI, unlike most of ganon's fight, but even compared to puppet gannon Majora had balls.  She didn't need no triforce or whatever just pure psycho bitch anger and it was great.  Changing forms Majora only lead me to having "ohhh shit" moments up until the last blow.

Truly a memorable boss fight.

Fighting Bowser from Super Mario Bros. 3.  Quite an epic battle the first time you got there and then the music and making Bowser put himself out of commission was an interesting way to win.

SPOILERS FOR SHIN MEGAMI TENSEI: DIGITAL DEVIL SAGA 2



God the final boss(You can pretty much tell the guys who made it are atheist) I remember full on expecting a extremely powerful being who is fucking huge..What do I get..A FUCKING TOWER WITH A MOUTH!!!!!

Not just that but the fight there is extremely boring you just fight four forms and each has its own element.
The reason its so memorable is because of how boring it was.

Digital Devil Saga 1 had a great last boss though check that game out but stay away from 2.

(You can pretty much tell the guys who made it are atheist)

Oh, that's just awful...