Panda Batch File Renamer is good and free. It'd probably be fine renaming them on the sd card but you could copy them to your PC if you're worried about corruption.
Smash Wii U is extracted with Sm4shExplorer and files are opened with Smash Forge. Ultimate is extracted with ArcExplorer and files are opened with StudioSB. There are guides on their respective gamebanana pages.
Don't know about 64, Melee or 3DS.