Funny how the Gorn made it in people's "best" list. I didn't really care for the outlandishly fake looking lizard incarnation, and the repetitive "clearing of the throat" type bellow from it was silly, but what really spoiled it for me was the narrow mindedness... attacking an outpost without fully understanding the capabilities of your potential enemy, and not even trying a diplomatic approach first ("hey, this planet is ours so you need to leave"). It could have been a basic message first, then after a few months of pause with no sign of the humans leaving, THEN attack.
Anyway, I'm also of the camp that I enjoyed most of the villains and would find it hard to pick a top 5. It's far easier to pick the failures.
1. Gorgan, "And the Children Shall Lead"
2. The evil Lazarus, "The Alternative Factor"
3. Dr. Janice Lester
4. Lt. Cmdr Finney
5. Dr. Sevrin