To crop out borders, use MeGui's AVS Script Creator.
Give MeGui the video file, select crop, and start cropping. You can use Auto-Crop, but it is not always perfect (sometimes will eat more than needed). Just adjust accordingly. Then go to the script(? Can't remember. Not on XP. It is one of the taps) and copy and paste the crop script
After cropping, maybe resize the video to a system's native resolution (for SNES, it will be 256x224)
crop(a, b, c, d)
LanczosResize(256, 224)