You’ll have to realize two things:
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Japanese RPGs aren’t as universally focused in modelling morality
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and they aren’t as focused on world-building as Western RPGs are.
Having said that, here goes the list:
Oni series - instead of a system of good and evil, ran on a sense of karma, you got bad karma for doing certain things, good for others and it followed you around.
Tokyo Majin series - Hideously complex dialogue choices. It was a combination of choosing from a number of dialogue responses and giving one of nine basic response types to a stimulus and it controlled what fights you got into, who came on your side, how well you worked with others in battle and the branches of the plot.
Weltorv Estleia - In this game, you could do anything from buying a house and getting married, to becoming a pirate, to becoming the new dark lord and terrorizing the land.
Soldnerschild - This game cast you as an up and coming in a country’s army, then throws you into a huge political conflict, how you react determines how the war turns out, how loyalties play and so on and so forth. In fact, I think this is the best representation of such an idea ever seen in a game, and goes way beyond similar ideas seen in things like Romance of the Three Kingdoms.
Z’ill Oll (Infinite too) - In this game, you had a soul with ratings that would rise or fall based on your actions (things like your bravery or purity), your soul woudl change and so would the game. Depending an ultima like beginning sequence, you could also start in one of six starting storylines and the way the soul system interacted with a guild quest system and a heavily, heavily branching storyline made for one open-ended RPG.
Ore no Shikabane wo Koete Yuke - You raise a family of many generations in order to get rid of a curse, the way in which you acheive this goal is veeeeeeeeeeeery open-ended and has a huge effect on the history and the gameworld.
Lolita Fantasy: Warty Penis Dreams - Just seeing if you’re still with me.
Romancing Saga 2 - Nearly all the Saga games are open-ended, but this I think, is, in the best way. It tasks you of taking control of many generations of a country and your actions in one generation determine the outcomes of future generations and it just keeps on snowballing.
Lunatic Dawn series - You can get married, have children, divorce, kill your wife, steal the kids and raise them to be the leaders of crime syndicates if you so wish. Your actions don’t just affect characters, but the ecosystem of the game too, having an effect on the land and towns development around you, as well as the populations and kinds of monsters. You can be virtuous, or get involved in the shady underworld. Lunatic Dawn games almost have too much freedom.
Venus & Braves - You play an immortal tasked with the burden of preparing against a great catastrophe in the future, time is at your manipulation. In this game you can CREATE the legend of the hero and the sword by manipulating the people involved and then manipulate the future youth who will find it. Party interaction is greatly emphasized over the course of many, many, many dozens of years.
Valkyrie Profile - Its well known by now, unfortunately I can’t really tell you what it is you can do in this game, as would consistute a massive spoiler and I wouldn’t dream of ruining the surprise. Beyond that though, I can tell you there’s a lot of leeway in how much you listen to Odin’s demands and what kinds of decisions you decide to make and when. It helps that this is also one of the greatest video games ever made. :P
Atelier series (note: excludes the Eternal Mana games)- You can have an effect on the development of your town, get involved or completely ignore relationships and developing storylines with any number of different characters, your reputation goes up or down, any number of possible goals are available, each with their own ending, etc.
Fire Emblem: Genealogy of the Holy War - This is, in my mind, one of the best examples of where open-ended design can get you. Sure you can’t do the campaign out of order, but that’s to the game’s benefit. What you can do is influence relationships and leadership to such a degree that the entire game’s second half is different.
Chester the Crab and His Adventures in China Vagina Land - Again, just wondering if you’re still paying attention. Sadly, this is an actual title over here, but not of a game.
Ogre Battle series - Whether you decide to be merciful and lawful or ruthless and reckless has a great deal to do with troops you can hire, what scenarios you get landed with, who will be your friend, how much people trust you and which one of the endings you get.
Since by this time everyone is well aware of the Megami Tensei games, I doubt I need to bring that up again. There are more, but I’m guessing you’ve got the point now. Japanese open-endedness isn’t always so much about morality, (though there are plenty where it is) its usually more about relationships and are some kind of dynamic unique to the game’s storyline.
In addition, here is a list of games released in the States where your dialogue choices do have an effect on the game:
Shin Megami Tensei: Nocturne
Digital Devil Saga 1 & 2
Persona
Persona 2: Eternal Punishment
Romancing Saga
Tales of Symphonia
Star Ocean 2 & 3
Riviera: The Promised Land
Suikoden II
Suikoden III
(I heard a story that the Konami Suikoden designers got so swamped in reaction mail from the “No really, I insist you drink this poison” dialogue “option”, that they vowed never to do it again)
Radiata Stories
Tactics Ogre
Front Mission 3
There’s also Suikoden IV, but I was trying to limit myself to good games. I probably missed a few, I can never quite keep track.
The only game besides the two in this thread I know of that’s coming out in the US that’s open ended is Ryu Ga Gotoku, though I believe its going to be called Yakuza. Its an action RPG. I can’t tell you in what way it is open ended yet, because I have yet to play it, I just know there’s a lot of leeway in what you can do.
You all read this far? Ha ha, you stupid! I just copy paste old Kitsune post! BANZAIIIII!