@Smeags: I was going to guess Wind Waker because of Ganon getting a sword in the head but then I thought there's no second antagonist in Wind Waker. Is there? Maybe it's been too long since I've played it...

You smash the Helmaroc King's head with the Skull Hammer (I was trying to make my hint less obvious).

As for the first hint...

#14

Ico

I adore Shadow of the Colossus -- it's also in my top 50 -- but I like Ico even more. Here is a unique masterpiece, a title that strips the action-adventure game down to the very basics. There isn't much story, much text, or much music, but there is atmosphere and emotion to spare. There is something very magical about playing through Ico, and it's hard to articulate. Maybe it has to do with the dreamlike quality of the game, the hugeness of the castle that creates a feeling of loneliness (even hopelessness), or the special relationship between Ico and Yorda. I'm not sure. All I know is that Ico is brilliant, and deserves to be mentioned along with the best games of the sixth generation.

Hint for #13:

A little Easter-egg before fighting a boss in this game: Do not disturb the waters... or tragedy will surely befall you. I learned that the hard way.

14. Monster Hunter Tri, Wii (2010) Capcom
Sometimes the Japanese are just wierd, and sometimes they have brilliant taste. One Piece is one case where they are right on the money, and Monster Hunter is another. You would think a game that requires you to grind monsters to acquire any sort of weapon or armor upgrades would be boring, and it can be boring in single-player (though still fun enough), but with online multiplayer you have something that just sucks the hours away. Epic fights, a wide monster variety, all sorts of weapons that offer different ways to play, the only thing bad about this game is Rathalos. Fuck that guy.

#14. Metal Gear Solid (PS1)

I don't care what anybody says, this is the best Metal Gear Solid game. The story is well constructed with nice plot twists, great intrigue and amazing characters. The whole cast was fleshed out, even characters you never meet like Naomi Hunter (who still had her English accent back then) had a backstory , most vilains left a lasting impression, Psycho Mantis being the one that impressed me the most but Liquid Snake, Revolver Ocelot, Vulcan Raven and Sniper Wolf were all awesome in their own way.

The gameplay was unlike anything I had played before, you had to think your way through, avoid being spotted, enemies could follow your footsteeps in the snow but were totally fooled by you hiding in a cardboard box. While the focus of the game was to avoid confrontation, when you did get in a fight, the combat system was more than adequate and boss fights were innovative and constantly different. On your way to the end, you find yourself fighting a tank, a helicopter, a sniper, a cyborg ninja and a bullet bouncing Russian.

To me this game had the perfect balance between great gameplay and captivating story which the sequels never manage to recreate entirely (Snake Eater came close).

#13 Hint: To finish this game 100% you had to go up to 96.

13. Damn this rainbow takes forever.

Mario Kart 64?

Really thought i had a good one that time :/