I can only think of the first Nintendo bosses:
The last boss of "Black Manta"
There was a boss in Megaman 2
Also another boss in "Street Figther" on Nintendo .

Street fighter 4 seth. first night with the game took me 2 hours to beat him with c.viper

Use your knife

I'm not sure about the hardest ever, but Shao Kahn from Mortal Kombat IX comes to mind in recent times. Good gravy that fight turned unfun very fast.

@Rol

That's probably the nicest thing you've ever said about me.

Namir from Deus Ex: HR. I did the option that unknowingly resulted in my whole HUD going dead. Oh, how I did rage. He cloaks all the time, jumps over walls, and throws grenades.

Jinpachi is hard? I find that Azazel from Tekken 6 is way harder than Jinpachi.

Man... I'm so sad now... I spent hours of my life on it.  =(

Thanks anyway.

Yeah, I hear ya.

I spent my entire Broken Butterfly cache to take him down. Only later on did I learn about that secret. And it honestly makes perfect sense! xD

Do you even Killer7?

Killer7 was awesome, but Broken Butterfly is unmatched when it comes to pure damage output (with upgrades of course).