I am not sure which game stories I would put down as "art" as I am not sure if they can meet the standards of other media that has such as literature. Mind you, I have never read literature so it could just be that a lot of these books and texts that are considered by critics and analysts to be the high point of writing, characterization, exploration of concepts and themes, or representing their zeitgeist is just a bunch of masturbation porn on their side to make them feel like some kind of literature "connoisseurs" of the written word who are above the rest of us plebes that do not grasp the greatness, deepness, and meaningfulness of these works.
Though I am sure that some works do indeed represent the pinnacle of craftsmanship and the writer's intellectual strength.
One problem I sometimes have with games that try to be "art" is that how disingenuous or pretentious, or should I say the people behind it are "I know I am an artist/genius and I am going to show it to you through some artsy-fartsy project, and if you don't get it or do not like it shows how stupid or backwards you really are", with as a result that a lot of people will praise it publicly because they don't want to come over as being imbeciles.
And of course more lately games that jump on the current social politics movements which almost automatically make them "deep and honest", and if you disagree you are an -ist or a -phobe. (I am sorry that I had to bring this up, it is almost like Godwin's law, but it had to be said)
All I can mention are games which storylines I felt were more memorable than those of other games that I have played. Some do indeed deal with philosophical subjects or try to tell a deeper story regarding certain themes but that is not a mandatory requirement for me to make it to my list.
- Anachronox (god does this game need a sequel)
- Snatcher
- The Secret of Monkey Island
- Indiana Jones and the Fate of Atlantis
- Deus Ex
- Planescape Torment
I am heavily divided on the Fallout games (Fallout 1, 2, New Vegas). I really like them but to call them art?
They are in general a lot better written than most contemporary games and a lot that came after them but I feel a little biased if I would put them down as art though I guess they do establish certain standards in gameplay connected with story telling.
Perhaps I should also treat the term "art" as what I feel it means. That it inspires thoughts and feelings in people who watch, read, or listen to it (or play it). It having an impact on people that lasts with them.
- Metal Gear 2 Solid Snake
- Timesplitters Future Perfect
- Metroid Prime 1/2/3
- Metroid Fusion/Zero Mission
- Star Trek 25th Anniversary/Judgment Rites