Metal Gear Solid 3: Snake Eater?

Incorrect!

More recent

   23

   The Legend of Zelda: Majora's Mask

   System: Nintendo 64, Nintendo GameCube
   Genre: Adventure
   Year: 2000
   Rank last year: 25 (^ 2)

 Being one of the most unique entries in this beloved franchise, Majora's Mask stands out from the rest. While it is one of the few direct sequels in the series, it takes a break from the usual story involving the Triforce, the Master Sword and Ganon. Majora's Mask instead takes the player into another dimension where a prankster (a familiar face from the game's predecessor) under the influence of a demonic mask holds the world in it's grip. The story has quite a deep meaning involving themes of friendship, when the player is able to read through the lines. Infamous is the game's 3-Day system. Personally I think it's a brilliant addition and it makes the game. Without it, it wouldn't be 'Majora's Mask' and the events in the game wouldn't have the same sense of urgency. Moreover a lot of those events wouldn't even be possible in the first place and I feel people opting to remove the feature never really understand what the game is about.

As a Zelda game, the gameplay is unbelievably tight and features one of the best soundtracks in the series. It's also one of the best looking games of the 5th Generation to boot. In Europe, we were also lucky enough to be blessed with this box-art, which I still think to this day is one of the prettiest box-arts for any game ever made. I clearly remember a bet with my mother leading up to the release of this game. When we first saw the tv-advertisement, we were unprepared and weren't sure of it said '27 hours to save the world' or '72 hours'. I said '72', and needless to say, I won!

Assassin's Creed 3

Game #22

This simple game from an IP at least famous in Europe, has it's gameplay based on the same board-game as another much bigger, grander franchise.

Even more recent.  It also isn't the third game in the 'series' but the two games before it was what people compared it against most

So, a top 50 list is very hard to make when you're playing games since 1992...
Here are 50 more games that could have been on my list in alphabetical order:

Anno 1404/Dawn of Discovery
Baldur's Gate
Batman: Arkham City
Beyond Good & Evil
Bioshock Infinite
Call of Duty 4: Modern Warfare
Castlevania: Symphony of the Night
Devil May Cry
Donkey Kong Country 2: Diddy’s Kong Quest
Doom
Final Fantasy VII
Gran Turismo
Grand Theft Auto IV (yeah, it's cool with mods)
Half-Life
Jedi Knight II: Jedi Outcast
Kid Icarus: Uprising
Mario & Luigi: Superstar Saga
Max Payne 2: The Fall of Max Payne
Metal Gear Solid 3: Snake Eater
Metroid Prime 2
Mirror's Edge
Neverwinter Nights
Paper Mario
Paper Mario: The Thousand Year Door
Pikmin 3
Planescape: Torment
Portal
Pullblox/Pushmo
No One Lives Forever 2
Resident Evil 2
Resident Evil Remake
Return to Castle Wolfenstein
Secret of Mana
Soul Calibur 2
StarCraft II
Street Fighter II: Turbo
Street Fighter Alpha 2
Stronghold Crusader
Super Mario 64
Super Mario Galaxy
Super Mario RPG: Legend of the Seven Stars
System Shock 2
Teenage Mutant Ninja Turtles IV: Turtles in Time
Tekken 3
The Curse of Monkey Island
The Legend of Dragoon
The Legend of Zelda: Link's Awakening
The Legend of Zelda: The Minish Cap
Tony Hawk's Pro Skater 3
Warcraft 3: Reign of Chaos

Yes, yes, YES!

#23 The American version of this game used traced stills of Arnold Schwarzennager from the movie Predator to display its 2 main characters on the box cover.

Contra