Well, the games weren't designed for that aspect ratio, though with a little openGL wizardry deep in the video plugins you could probably change the camera properties to see "more" at the sides of the screen. But there would be a lot of undefined behavior. Highly optimized games might not render that stuff on the sides of the screen if it's outside the original field of view. Also the UI overlays in the original game (menus, icons) might be problematic. This has been discussed briefly on the forum elsewhere, you could probably dig it up and resurrect the thread if you want.
One game that already does support a form of widescreen is Jet Force Gemini. In the in-game settings, change to widescreen display. Then in Mupen64Plus-AE display settings, change "Screen scaling" to "Crop". That virtually eliminates all black bars and distortion. But that's obviously very game-specific.
