I found both the post by Kiss-Shot and FappingFury to be amazing, it helped me to see what they saw in the games they mentioned, though i played the first bio shock and bits of far cry too, bored of it(far cry 2).
Atmosphere...
i loved the atmosphere of Resident Evil 4 and Dead Space, if i wasn't careful i would be sucked in and scared, which for some twisted reason i enjoyed. oO
Character's...
Shinning Force Exa
i loved the 2 characters (Toma & Cyrille) who started out bitter towards 1 another but being forced to fight along side 1 another they become friends and b4 they realize it they'd had fallen in love with each other, which i loved to play through.
Disgaea
the humor that no matter how many times i replay is always funny and character development/growth between Flonne, Laharl, and Etna... the cold hearted demon lord Laharl, the unfeeling/back stabing demon vassal Etna, and the ever so ditsy love freak angel Flonne.
Mana Khemia
i had the hardest time choosing the girl i wanted to end up with but when i choose Nikki and i saw the her ending it had given me a warm and fuzzy feeling.
Atelier Iris
the game felt more like testing there new engine rather than a game(crap pretty much), but i fell in love with 1 of the side characters (female) who develops an interest in the main character, she starts off bitter biting at everyone but if you choose to help her she slowly opens up to you and i couldn't resist struggling to find the next item she needed to further on the story between her and the main character.
Story...
Tales of symphonia
was an amazing story that was never predictable for me, constantly evolving, constantly changing, by the time i was half way through it felt like a different game from the 1 i started, i enjoyed the growth of the main characters Lioyd and Colette and the hardships they struggled through to stay together.
Skies of Arcadia
it is one of my first jrpg's (in all my years of gaming, gaming since 3) and once i picked that game up i could not put it down, the music was fantastic, the story was amazing and enthralling, the characters were fun and i felt for them on an emotional lvl... what am i talking about was, i'm still playing the game even now... 3rd or 4th play through, nothing new happens when i play it again, i play it simply cause i enjoy it. there is nothing they could change to make it better
Wild Arms 2
i played it awhile and for that reason i cant remember much about it, but till this day for the last 2-3 years i have been searching for that game in game stores every time i go, i have deeply regretted losing that game to the point i could hate myself, i don't know what it is that drives me so, but that game haunts me
i would also like to add Persona(3 under my belt), Xenosaga(1&2), Dark Cloud 2, Baten Kaitos:Eternal.., Sword of Mana(made me cry at the end), and Golden Sun(both),(wish they made a 3rd game), those who have played them should understand why.
an 1 odd ball id like to add, Grandia (the first, friend has my 3rd, b4 i got to play it too...)