I guess I'll give hints to my first few games as well, though first I'll mention the games that fell off my list this year.
Ratchet & Clank: A Crack In Time:
Still a great game, but with some shuffling happening and a few new games entering my top 50 It just fell below the cutoff point.
The Legend of Zelda: A Link to the Past:
Last year A Link to the Past fell three places to #47, and unfortunately this time it went down four places and just barely out of my top 50. Maybe if I replay it some day the game could make a return, but as things stand, there were just 50 games I felt more strongly about when I was editing my list this year.
Now for the first few hints:
-This game is a continuation from the fifth possible ending in a game called Drakengard.
-In the mind of a dying man.
-To finish the game you need to shoot a small hole in the moon.