Dr. Doom has always been a top pick for me. While considered a villain Dr. Doom had Earth’s best intentions in mind. He saved the Earth many times. The country he ran Latveria did very well and did not suffer from many of the same fates every other country fell into.
Darth Vader- is another great one. A very complex villain who we learned so much about. He has to be mentioned in my list.
Thanos- Thanos was one I have enjoyed since long before MCU. Thanos was also a very complex character in the MCU movie. I really like how they did Thanos in the movies too. In the comic books Thanos was like the ultimate SIMP! He simped for Death so much that he killed half of the universe just to gain her affection. Infinity Wars from the comic books was more of a love story between Thanos and Death. However Death like most women wanted the one person she couldn’t have. That was Deadpool.
Deadpool – While not a typical “villain” he is not a good guy either. For a long time there he was considered villain status. I just enjoy his humor and crazy attitude.
Sauron – He goes without saying. True badass!
Megatron – Love Transformers and there was always more to Megatron than just the evil leader. He had his reasons for being who he was. All hail Lord Mega Tron!
Star Scream- The true villain of Transformers. Always trying to take Lord Megatrons place. I enjoy Star Scream for what he is.
Sound Wave- Always the loyal one with lots of fun minions, Ravage, Laserbeak, Buzzsaw, Ratbat, Rumble, Frenzy, Slugfest, and Overkill.
I just love all the cons as villains. They always had very solid Decepticon
Cobra Commander – Grew up on GI Joe. So had to toss him in here along with Destro, Old crome dome himself!
I am sure I am missing out on lots of other greats but that is my top list from the top of my head.