Ergo Proxy
If Ergo Proxy had come out before Oni instead of in 2006, it could definitely have been a formidable influence on the game. As it was, Nausicaa was an influence on Oni, as stated by Hardy LeBel, and this is seen in the concept of a wilderness that is hostile to human life, an "outdoors" that is fundamentally toxic to us. Ergo Proxy takes place in the same kind of world. The reason for this pollution is eventually revealed in the show; it comes as no surprise that it is man-made.
No one alive has seen a blue sky, or the sun. In order to survive, humans have crowded into domes around the world. Each dome is somewhat distinct, though we learn little about the domes besides Romdeau (a distant future corruption of "London"), where the story begins and ends. Romdeau is a highly-controlled city-state with citizens calmly walking to and fro while being urged by billboards to consume and dispose of goods (the waste being dumped out of the dome in large streams). It is a utopia in the sense that no one seems to have any wants (nor any questions) about their world, and which the main character calls their "final paradise".
The icing on the Big Brother cake is that every citizen is in fact designed to perform a certain function in society. Natural childbirth has not occurred within memory; citizens are birthed selectively by a mechanical womb system. This system also helps prevent overcrowding. Get a promotion, and you may be rewarded with an allotment of one baby. The population of the city is technically about 50% Auto-Reivs, which are various kinds of robots. An especially sophisticated type called an Entourage is a very intelligent but clearly artificial android which accompanies its owner and handles a lot of the human's duties, to the point that many of them are essentially doing their masters' jobs.
There's trouble in paradise, though. A virus is making the Auto-Reivs self-aware, and there's things called Proxies running around killing people. When two Proxies meet each other, their mutual hostility is even greater, not unlike the meeting of two Daodan symbiotes (if Konoko vs. Mukade is any indication). Many philosophical, linguistic, historical and artistic flourishes, as well as fleeting visual symbols (like butterflies, of note to Oni fans), make this a show to watch carefully and thoughtfully. Re-watching it once or twice is a must in order to grasp certain aspects of the plot (and turning up your TV's brightness helps a lot too!).