I'm away for a few days, so I'll post more hints and keep delaying the write-ups
#48 - This Zelda-like has you go from its hub town to the 4 directions around it, wherein lie gigantic beings. It's not Majora's Mask!
Hint 2 - You play as a blue-skinned swordsman.
#47 - This other Zelda-like starts you off in a completely grayscale area, from which you travel through doors to the "real" world.
Hint 2 - You play as a crow wielding a sword that glows red.
#40 - A game that was made to appease North Americans' desires of gritty "mature" realism.
#39 - The first entry in a sci-fi trilogy that is almost more well-known for one of its supporting characters than the main character.
#38 - The only numbered sequel in the mainline series of a franchise over 25 years old.
#37 - Possibly the most maligned game of all time, but even it is having somewhat of a redemption arc.
#36 - Though it is the third game in its series, it's often treated like it was the first.