For me there are none. But prior to experiencing Dark Souls i had very high regard for the following:
Shadow of the Colossus - A great work - perhaps PS2 finest game - and perhaps closer in spirit to Dark Souls than most.
Dark Chronicle (Dark Cloud 2) - a gorgeous and very fun and playable RPG.
Dragon Quest 8 - ditto.
Bioshock - beautiful and haunting FPS set in a wonderfully realised dystopia
Half Life 2 - Another thoroughly absorbing Action Adventure.
GTA Vice City- Music, Style, freedom, a very entertaining sandbox game.
However - none of the above could i consider to be works of genius that transcend their medium. Dark Souls on the other hand can be compared with any great work of art and stand up well against it imo