I don't think I have any. No fighting game boss really standed out to me.
Since I have to choose, I think I'll say TT2's Unknown boss fight. Very reminiscent of Majora's Mask and PSO.
I liked her TTT boss fight with that floating wolf, the stage and music gave it a really dark vibe I loved. DOA1 Kasumi vs. Raidou in Dimensions round one with Ketsui no toki was also a fav..."Raidou...This is for Hayate!"
fighting game bosses normally suck, honestly. Are we talking about gameplay or just setting and such? Marie is an awesome final boss for Skullgirls visually and fits the tone, but the fight itself is not great.
That's a tough one. Bankotsubo in DOAU is pretty hype, I-No in GGXX is also awesome, Vold in Fighting Layer gets a special mention. But If I had to pick the most memorable, to me? I'd say Shin Akuma in SFA2 Gold takes it, because dat fucking music tho.