Metal Gear Solid 4: Guns Of The Patriots
While it may be famous for its long cutscenes, MGS should also be known for it's Crazy bosses. It is also hailed as the most difficult game in the series, which is saying a hell of a lot!
Gears Of War 2
While not as satisfying or hard as the First GOW still proves that there's no such thing as a Sophomore slump for a video game Franchise.
Megaman 9
No, this is not a mistake or joke. This game did come out this year, the graphics really do look like that, and yes this IS the hardest Mega Man Ever. Anyone who has played the first 3 Mega Man games needs to play this. Proof that you should never judge a game by graphics. Go anywhere on the internet to find the toughest games of 08, I bet every forum you go to mentions MM9 at least a few times.
Fallout 3
While the game doesn't have a ridiculously hard ending boss, it still is freakishly hard to beat, especially on a harder Difficulty. While not substantially the hardest game of the Year, Fallout 3 is anything but easy
Ninja Gaiden 2
In true Ninja Gaiden Fashion, this game is FUCKING HARD AS FUCK!!!! You WILL lose your cool at least a few times playing this game..... Picture Through the fire and Flames Hard, that's how hard most of the bosses are in this, and basically any Ninja Gaiden Game through time.
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I wish I could call a tie between Megaman and Ninja Gaiden, Megaman isn't as complete of a game as NGII. So I'd have to go with Ninja Gaiden II.