To run in 16x9, the game has to support it (like F-Zero GX and Soul Calibur II). There should be an option somewhere to change it.
If a game doesn't support 16x9 then (it depends on how good your TV is but) you can probably stretch and/or zoom in on the picture so that it takes up most of the screen. Alternatively, you could have an unstretched picture with black bars on the left and right side of the screen. That's how I prefer to play it - I don't like to stretch the image or zoom in so that I miss something on the top or botom of the screen.