Short answer is that all the 35mm and 50mm prime lenses are good ones.
The difference between AF and AF-S, is that the AF-S has a built in silent wave motor (SWM), whereas the AF lenses require a motor in the camera body to drive the auto-focus.
The D90 has a built-in AF motor, so either AF or AF-S is fine. AF-S might focus faster.
Inside focus is nice if you are using a circular polarizing filter (CPOL) because focusing won't change the orientation of the filter after you have set it.
Spending more for the F1.4 versions is really up to you, and how you plan to shoot. If you are shooting in low light, and/or you want more depth of field, it might make sense to get the F1.4, but I think F1.8 is pretty good (especially for the money).
The D90 is a DX (cropped sensor) camera, so the effective focal length multiplier is 1.5x (meaning the 50mm lens is like a 75mm lens on an FX camera like the D3, and the 35mm lens would be like a 51mm lens). Many people call 50mm a "normal" focal length, so on the D90, that leans toward the 35mm with its 51mm effective focal length.
I bought the 50mm F1.8 for my D90. It was really great, but I found that it wasn't as wide as I would like for what I bought it for. I was taking Tae Kwon Do shots at my son's club, and I found that the club was small enough that I couldn't get far enough away to get them in the frame for some shots. The 35mm would work better for me.
I wouldn't worry about the G (lack of aperature ring) unless you plan to be using older cameras.
Best of luck with your decision, and enjoy your D90!