I would count the Romulans in "Balance of Terror". Even though they were interesting guest characters with differing motives, they were all given orders to attack and kill and they obeyed. In the end, as "human" as their Sarek-like Commander may have been, he still chose self-destruction to avoid being taken into Kirk's custody; he voluntarily killed himself and whatever other survivors there may have been to keep the Romulan ship and personnel out of Federation hands.
Anan 7 ("A Taste of Armageddon") was another bloodthirsty aggressor. He regarded the Enterprise peace mission with contempt and was prepared to fire on the ship without provocation, seize the landing party, and threaten to kill them as hostages. The Eminians in general, despite their human-like moments, are easy to judge as villainous because of their blind devotion to computer-sanitized perpetual warfare.
The Gorn in "Arena" were definitely villains. It was only the Metrons' interference that gave Kirk the opportunity to both stop them and show mercy, opening the door a diplomatic solution. Without the Metrons, Kirk would have either had to catch up with the attacking ship and destroy it, or risk a continuing conflict with the Gorn. It could be said that the Cestus III colony was an intrusion, but the Gorn applied violence and treachery from the get-go instead of diplomatically confronting Commodore Travers.
Landreau ("The Return of The Archons") was a computerized villain. C-111's Beta III could legitimately be called a starship trap and its mind-control technology, left in the wrong hands, would be a major threat. There was no human paradise there. It was just a cyber-dictatorship.
Khan Noonian Singh, as seen strictly in "Space Seed", was diabolical. He was another Hitler.
The flying rubber barf critters on Deneva ("Operation: Annihilate!") were parasitic like ALIEN, but Spock and Aurelan made it very clear they knew what they were doing. Kirk gave them the demise they deserved.
Harcourt Fenton Mudd was always a delightful villain. Maybe not a monster, but the kind of con-artist who somehow got into deep space and became a kind of low-grade menace. I always wanted to see Kirk phaser-stun him and throw him in the brig.
My all-time favorite villain was protected from retaliation by the Prime Directive and he knew it: Proconsul Claudius Marcus of "Bread and Circuses". This is a ballsy, Putinesque plutocrat who stood toe-to-toe with a Federation starship captain, jailed him, tried to coerce him at gunpoint, and arranged his execution before Scott's electro-magnetic pulse intervened. In the end, even his loyal henchman Merrickus had enough and used a communicator to save Kirk and company, sacrificing himself to escape his Roman trap and Kirk's scorn. For Captain Merrick's troubles, the Proconsul did what Putin himself would surely admire: stabbing Merrick in the back with a knife. I often wondered what happened on that planet after Kirk and his party were rescued. It may be a perverse fantasy, but what if Kirk's intimacy with Drucilla resulted in a weird cross-species STD that she would germinate and spread to Marcus, leaving behind a kind of perverse kissoff for him to think about...
Bele and Lokai were indestructible villains, and their own worst enemies. By leaving them in the ruins of their homeworld, these feuding villains imprisoned themselves much the same as Kirk did to Lazarus.
"The Lights of Zetar" gave us another pure and deadly villain, capable of killing everyone on a ship or station. They valued only their own lives and respected nobody else. Kirk again furnished their demise, and nobody felt sorry for them.
TOS wasn't really about furnishing villains for a Mel Gibson-style slaying like you would find in LETHAL WEAPON. From the beginning, TOS made it clear it wasn't about sending the Enterprise on a righteous crusade to rid the Universe of evil. Kirk did slay some mighty monsters, such as "The Doomsday Machine", but these were often either mindless technology run amok or they were single-minded obsessive aliens like "The Gamesters of Triskelion" that Kirk had to match wits with to trick them into ceasing and desisting. More often than not, though, Kirk found a clever Deneva / Zetarian demise for them.
