The game where it's a rich guy that sends a trained assassin out onto a island with nothing and hunts him for 24 hours, and if the assassin kills the rich guy he gets his freedom and like $20K.
The NES & arcade versions are very similar in terms of level layout and enemy spawns. There are certainly differences, but I haven't played the arcade version enough to tell you what those specific differences are.
I personally enjoyed Total Annihilation, but Planetary Annihilation and some of the later games, like the Spring-based remakes never quite caught me the same way.
The arcade was the original version. There's also a really good modern port on the Commodore 64 with a banging soundtrack called "Ghosts n Goblins Arcade"