Supposedly Yuji Naka programmed an emulator that would run the NES Super Mario Bros on the Mega Drive for his personal use way back in the late '80s. That's from an interview on shmuplations. But as far as public emulators, yeah it's probably NesTICLE or Zsnes, whichever came first. One of the first I ever used personally, back in the day, was MEKA, which was for Master System and Game Gear. Came out in 1999 and was very good at the time. I remember using Genecyst as well and having sound issues. Then Gens made it obsolete, and eventually Kega Fusion seemed better.