Go to the SFC3 folder (usually C:\Program Files\Activision\Sfc3).
There should be a file titled either "Orig.bat" or "Original.bat" (you might not see the .bat, depending on your Windows Explorer settings). It shows a little window with a gear in it for the icon.
Double click Original or Orig, a little DOS box will appear briefly and disappear (with a fast computer you probably won't have time to read it), and the game will be restored to original.
There will be another batch file to turn the mod back on.
Most of the major mods have these: Pelican's DomWars mod, Chris Jones' TNG Mega Mod, and (after I made the GFL ones) the new GFL mod update, and my new Sci-Fi Bashfest mod. Some mods don't (last I checked, TNZ didn't, though they might by now), but those 4 mods I listed will have batch files to swap between them.
You can download my ST vs SW (Sci-Fi Bashfest) mod here if you're interested, it has batch files as well
http://forums.taldren.com/ubbthreads/showflat.php?Cat=&Number=331142&page=0&view=collapsed&sb=5&o=&fpart=1