Absolutely.
GenesisGX, any of the Beetle cores which are just Mednafen renamed, any of the SNES versions (Snes9x, Higan, BSnes and Mesen S), Mesen) and Flycast for Dreamcast.
IMO Retroarchs universal shader and audio driver make it superior than the stand alones, on top of that you have Retroarchs input latency reduction features like frame delay and even run ahead if you want to dive into that.
The only emulators I don't use Retroarch in place of their stand stand alone conterparts would be Mame, Dolphin and PPSSPP. I still prefer the stand alones for those.