First, using S-video input (or composite) can only deliver 480i 4:3 images. I don't see how those images from your Nintendo players can possibly stretch to fill the entire horizontal width of the screen if your screen mode is "normal". This is a non-stretch, non-zoom setting, so it's beyond belief that it is not appearing in 4:3 form with black bars on left and right.
Now I'm not a gamer and I own zero gaming consoles, so I know nothing about setup or configuration options they might possess. But if there is a setting on your Nintendos that determines how to send out images, what do you have them set to. Are they supposed to be in 4:3? Do they only have non-HD outputs? In other words they cannot generate rectangular output, but only 4:3? Again, if that's true, then your 960 is doing something very odd by stretching a 4:3 image when it is set to "normal". Should not occur.
Instead of using the user menu to display things, if you push the DISPLAY button on the remote when something is on the screen from some input, you should also see onscreen information showing the input, zoom mode, input resolution (e.g. 480i), etc. You don't need to post pictures, just confirm that the 960 believes it's presenting "normal" output based on this onscreen DISPLAY. Again, "normal" should not be presenting a 480 4:3 image using up the entire horizontal width of the screen.
Second, using component video from your Xbox, Wii, and PS2, well now it's more complicated. Component video (INPUT6) can support all resolutions, both 480i 4:3 as well as HD 720p/1080i 16:9. So now it really is up to the configuration on the source devices what is being sent to the 960.
If these three boxes are also delivering 480i 4:3 over component video, then the presentation behaves as described on page 58 of the manual.
Again, if you use the DISPLAY button on the remote I'm curious to know (a) what resolution is coming out of the source devices, and (b) prove that it is in "normal" mode. As shown in my earlier post of pages 58+59 of the user manual, the presentation from component/HDMI input is primarily controlled by the source device setup/configuration and resolution of the source content delivered. After that, the screen mode button on the remote of the 960 can further influence things... but it depends on what the original source looked like, and the results are as shown in the manual. Or rather, they should be.
In any case, "normal" should not stretch anything.
What happens if you connect these players to a different TV? What do the various images look like on the screen?