Clue for 16: This game is part of a relatively popular franchise and took the series back in time.

Ratchet & Clank Future: A Crack in Time.

A good guess but no!

Hint 2: The developer is a relatively well known Japanese dev.

Kingdom Hearts II.

Nope. The series, whilst completely fictional, is set in the real-world and the game itself doesn't feature time travel. More of a prequel.

Metal Gear Solid 3.

Correct!

Just updated a whole bunch of games and caught up

1.   

• 41) COD: Modern Warfare (PS3) - Really fun and intense single player. Multiplayer that rewrote the rules of the trade. 
• 40) Need for Speed: Underground (XBOX) - Loved the customization and semi story based single player. 
• 39) Metal Gear Solid: Twin Snakes (GCN) - My first Metal Gear game and it rocked my socks off with its over the top cutscenes and gameplay. 
• 38) The Walking Dead (PC) - Set the bar for story based games in the medium. Brought me to brink of tears many a times. 
• 37) Wii Sports (Wii) - It puzzled me when i saw it but than i played it and had one of the most fun. Simple and puts a smile on ones face.
• 36) New Super Mario Bros DS (NDS) - One of the favourite games of all time born again on DS with oh so pretty colours. 
• 35) Metroid Prime 2: Echoes (GCN) - The only metroid i've played and it was an amazing experience. The music, the visuals and puzzles were oh so fun. 
• 34) Heavenly Sword (PS3) - Probably the first PS3 game i played and it took a while to beat the emotion captured on character's faces. 
• 33) Alan Wake (PC) - Made my Remedy. The atmosphere is simply amazing. Not too scary but just right. The writing is so good. Enter the twilight zone. 
• 32) Brothers in Arms: Road to Hill 30 (XBOX) - Found this game really hard and really rewarding. Strategic first person shooter. Very grim and very good. 
• 31) Yoshi's Island (SNES) - One of the best level designs in video games. Plus Yoshi Rocks. 
• 30) Burnout Takedown (XBOX) - The speed and exitement of arcade driving games brought down to the very core. 
• 29) Mario & Luigi: Bowser's Inside Story (NDS) - This game was so simple and funny. Really had a lot of fun. 
• 28) Left4Dead (PC) - Valve's take on zombies. Really fun game to play with friends. 
• 27) Aladdin (NES) - Loved this game as a kid. Played the hell out of it. Throwing apples at enemies like a mexican apple thief. So awesome. 
• 26) GTA: San Andreas (PC) - Took me a while to finish this but a ride it was full of colourful cracters with their own agendas. Gameplay was great too. 
• 25) Road Fighter (NES) - Spent so much of pocket money in arcades. Beats most modern games with speeds upto 400 kms or was it miles. :D
• 24) Elite Beat Agents (NDS)- One of the most bizzare and fun games i've played on DS. Just cheers you up. 
• 23) Resident Evil 4 (GCN) - This game creeped me but the shooting was so well done at the time that i had to rent it again and finish it. 
• 22) Contra (NES) - Another one of those childhood gems. I hardly could beat the game with 3 lives but beat it multiple times with a bit of konami code help. 
• 21) AC 2 (PS3) - The gameplay is simple but the fact that i could travel back to the cities of the past and experience them like a beautiful dream was great.
• 20) Max Payne (PC) - The bullet time blew my mind. Matrix games should have learnt a bit or two. The dark humour is still great to this day.
• 19) God of War (PS2) - This game is just insanely fun. Makes you feel like a complete bad ass and constantly adds new gameplay elements. 
• 18) Journey (PS3) - One of the most beautiful games i've ever played. Bit over 2 hours in length but the emotions it induces are priceless. 

17. Portal (2007)

Down from 10th largely because I'd play it's sequel if I wanted to revisit this type of game, this may be the game that makes me give the FPS a second chance (computer aiming seems far simpler than console for someone poor at multitasking).  The wonderful physics puzzling of the portal gun progresses nicely, teaching you all of the different things you can do with your "weapon" at a reasonable pace.  GLaDOS is nearly a perfect character (honorable mention to the turrets) with the writing for her character, and the song in the end credits alone is almost worth the price of the game when its discounted (often).  The game didn't overstay its welcome with the part after the test chambers becoming less straightforward but still using what you had learned.  As a result of how good this game is, I couldn't wait for the sequel and the addition of new mechanics and forced me to buy my first gaming computer.

Okay, I'm super far behind, but let's play catch up.

50. Maintaining Sanity is just as important as staying alive in this game, which almost never released. However who could blaime the protagonists after what they saw.

49. One of the first games, by a newly merged company, this was a violent game which involved the slaying of hundreds by sword or dragon. Had multiple endings, all of which are viewable on a single playthrough, each of which getting more bizzare with an ending representing a different outcome. One of the main Villains was actually your best friend who gets corrupt with jealousy over your Dragon and links with his own.

48. An under-appreciated SRPG which tells the story of a war from the perspective on honest fighters on both sides of the war.

47. A post apocolyptic treasure which featured slow motion exploding headshots.

46. A precursor to CoD, one of the best online shooting franchises.

45. Often Regarded the best game ever made.

44. One of the most well known voice actors brings a unique sense of comedy to this Treasure Hunting sequel.

43. Often regarded as one of the best games of all time, the main character is an iconic trademark which almost saw exclusivity on an opposing platform.

42. You only have 3 days left.

41. This marks the first Major spinoff off a traditional iconic series.

I'll add more games as people guess these correctly. I need to work to 15 right? I think my 2012 list is a better reflection of my tastes then my 2011 list, which gave new titles more respect then they actually deserve.