Will post my top 50 here, though I won't play the hints game because I'm very bad at making hints that aren't too obvious :P
I'll start by giving some honorable mentions:
#60 - Kirby's Return to Dreamland
#59 - Assassin's Creed II
#58 - Uncharted 2: Among Thieves
#57 - Ratchet & Clank Future: Tools of Destruction
#56 - God of War II
#55 - Pokémon Emerald
#54 - God of War III
#53 - Sonic Generations
#52 - Ratchet & Clank (2016)
#51 - Mario & Luigi: Bowser's inside Story
Now, the top 50. I won't do long write-ups cuz I'm lazy :P but I'll briefly mention some of the aspects I enjoyed the most about each game (I won't mention things I disliked because I don't want to be negative 
)
#50 - Kingdom Hearts 3D: Dream Drop Distance
What I like the most about this game: The combat system (fun, even if flawed), the worlds selection (especially the world based on the movie "Fantasia"); the flow motion, which makes you super agile; the soundtrack. P.S. I don't think the pokémon-like system is as tedious as some fans make it out to be.
#49 - Bravely Default
What I like the most about this game: The combat system, the job system, the soundtrack, the visuals. Also, Ringabel is the best character.
#48 - Dragon Quest IX: Sentinels of the Starry Skies
What I like the most about this game: The job system, the combat system, the story vignettes for each town (some of them are really moving).
#47 - World of Final Fantasy
What I like the most about this game: The stacking system, the ATB turn-based battle system like in the old FF games, the two protagonists and their interactions with iconic FF characters, the side-quests involving FF characters.
#46 - Dark Cloud 2
What I like the most about this game: The town-building system, the side-quests to get NPCs into your towns, the art style, the soundtrack. I must mention that this game has my favorite fishing mini-game ever.
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