For arcade version it's Raiden's, because of thelightning and lot's of blood. For Sega Genesis it's Sub-Zero's because in this version the blood keeps dripping down the spine after the fatality for a few minutes, also if u keep the continue screen counting down for awhile (maybe longer than 10 min, i forget) you will see one more blood drop come down. Very cool when I first discovered this. The first fatality I seen was Scorpion's Burning Breath on the Sega Genesis, seeing that Scorpion had no flesh on his head, only a skull and that you could do that in a video game was very kool. It wasn't just the fatalities that got me hooked on MK, it was everying coming together so well. The awsome character designs, background graphics, unique gameplay, hidden character/levels/secrets that went to town with my amazing imagination at that young special age, etc, etc.
Rest of my favourite fatalities in descending order for the arcade are: Sub-Zero's, Scorpion's, Kano's, Cage's, Kang's, and Sonya's Scorpions rip-off fatality as my least favourite.
we were all amazed back in the days ;D