Ico -
the scope (I remember looking down from the Flamelink Shrine for the first time thinking "This reminds me of Ico!"),
the hidden lore
the sense of the ancient
Shadow of the Colossus -
similar to Ico but also with epic boss fights
Ninja Gaiden (last gen) -
the precision fighting & various styles linked to different weapons
the hidden lore - the story didn't make much sense, but it seemed like it could have I remember reading item descriptions and wanting to know more...
the difficulty
Onimusha -
Haven't played this game in years but if I remember right, the combat and interaction with the world in general felt a bit like DkS
Vagrant Story -
the interlinked levels - masterpieces in both games
environment / ominous feel
abundance of realistic weapons
rich lore/story with profound conflicts
feeling of vastness and awe
Gothic 1&2 - this one is a bit of a stretch, but the difficulty / lack of handholding in these games was so refreshing. Also, few games have given me such a sense of accomplishment. This, DkS, and Indiana Jones on the Atari 2600 - making my way through that confusing mess of a game was a true accomplishment!