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As far as I know, Muto's site has not vanished. Actually, I just checked it now. It hasn't been updated since September of last year though...
I don't know if he is still working on YAD-S, but it does appear as though he has popped up recently in another forum somewhere, so it seems as though he is still around.
Returning to the original topic, I have used a game scripting engine known as Sphere a few times. It's a bit difficult at first, but it's basically just Javascript with some Sphere specific commands, it seems. It was developed with RPG's in mind, but I think it could be used for other types of games without too much trouble. I think their site is sphere.sourceforge.net.
I'm not sure about any other systems, but I have heard someone was using the Verge game scripting engine to make a ren'ai game. It seems mostly similar to Sphere, but it looked like the development of it was in chaos, last time I saw.
That's about all I know.
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