NES VC Injection: https://gbatemp.net/threads/release-ultimate-nes-vc-injector-for-3ds.437415/
SNES VC Injection: https://gbatemp.net/threads/release-ultimate-snes-vc-injector-for-3ds.453891/
GBA VC Injection: https://gbatemp.net/threads/restoring-original-colors-to-gba-vc.427642/
Color restoration: https://gbatemp.net/threads/restoring-original-colors-to-gba-vc.427642/

The ultimate injector covers most of the color restoration guide. Beware ghosting removal, it can cause burn ins on your 3DS screen. Use at your own disgression.