Hardest game you have ever beaten

Ninja Gaiden 2 (16-bit era), i think.  
God of War 2, also.

I wanna say Kingdom Hearts 3D. For whatever reason, the last world was a substantial step up in difficulty. Although I still think I might have been underleveled somehow.

I know I’m forgetting something, but for now I’m saying MGS3 on European Extreme.
 
I’ve beaten the hardest difficulty of many a game, but nothing quite like that.

@HeroInferno
 
I’m also going to have to go with yours.

Whichever game fits the two criteria;  
It’s not made to be ‘accessible to a large audience’.  
I’ve just picked it up and thus don’t know the mechanics of it.

Still no mention of Touhou. I must say I’m surprised. Either no one here has beaten it or no here has played it. Oh yeah, Sonic 2 for Game Gear was also very hard but I finally beat it after many tries.

MGS4 getting Big Boss rating.

Contra III - Hard Mode (3 lives only)
 
Super Meat Boy (108% completion)
 
I’m sure there are waaaay harder games that I need to get my hands on though.