Oooh good question. Tragically I am incapable of making a top 20 even if unordered so instead I am gonna start typing cut myself off arbitrarily at around 5000 characters

Arakune from Blazblue is a really interesting villain. He isn't the main villain from blazblue (who is also really good and well written) however Arakune is my blorbo.
Arakune is a sentient bag of bees who eats people and magic artifacts while laughing maniacally and summoning the entire bug population of Australia upon the opponent.
H... ..lks... .ke.. thi.. just constantly cutting out like he has a bad internet connection, or choking on something and keeps switching between surprisingly verbose to constantly repeating things and being as direct as possible.
He used to be a scientist named Roy who went insane over gathering as much knowledge and fell into the boundary (magic radiation dimension thingy) and then came out of it as a weird goopy tar thing with the only human element being the mask that he made back when he was Roy.
And for like 3 games straight that's pretty much all we really know about him, with some hints at humanity being thrown here and there but presumably he has lost most of his mind. But then it is revealed that nope Arakune could actually shapeshift back into his human form and he is doing all that by choice and he just really likes being a goopy bugman.
Such a funny subversion on the ol' "ooh tragic monster" archetype by having him go "yeah no I could go back I just don't feel like it anyway time to eat someone :D"
Oh and all his moves are named after different science formulas.

Doctor Neo Cortex from Crash Bandicoot is a such a pathetic wet napkin.
Like he does everything that other mad scientists do almost like filling out a check list
1. Try to take over the world with some sort of animal army ✅️
2. Convince someone on the opposing side to help you out with a scheme ✅️
3. Meddle with a more powerful mystical/magic force in your world domination efforts ✅️
And then he fucks up all of those.
He creates his biggest adversaries while building up said army.
The only reason why he convinces Crash in crash 2 to help him is because Crash is dumber than a box of rocks who will probably do anything you tell him to before forming 1 thought.
And he immediately becomes the equivalent of an assistant middle manager to the first demonic force he tries to invoke, and Uka Uka isn't even particularly strong.
Cortex is such a funny failure one just can't help but love that he continues trying to be the archetypical mad scientist.
Also my main in both Crash Bash and CTR. (Not that there is a difference between any of the characters in Crash Bash).

Daniella from Haunting Ground (or Demento in Japan) is an evil and intimidating lesbian and also the actual best character in the entire history of survival horror.
She is the maid at the castle where the game takes place and at first she seems like she has her maid priorities as she seems to just tend to her duties and even serve you 12 bowls of soup only for Fiona to leave the room without eating because she was not hungry. Anyway then she literally watches you sleep, starts having a mental breakdown the moment you wake up, bashes her head against a mirror, grabs the biggest shard, kisses her reflection on the lips and begins trying to kill you while giggling (real cutscene in the video game)
Most her insecurities all stem from internalised misoginy and it is really fascinating and well written how she berates and attempts to murder Fiona while sometimes stopping dead in her tracks to go back to her maid duties and trying to be Prim and Proper fore she knows that Fiona has literally everything that she wants to be yet her internalised understanding of how she Must be and what she Must do constantly clash with all those feelings.
She is the second stalker enemy encountered in the game who unlike the first stalker enemy has a functional brain and will constantly remind you because unlike what the game has taught you up until that point. If you hide and she can't find you and then leaves the room and the giant italicised text tells you "coast clear", it will not be coast clear because she can literally stop and stand right outside the entrance to the room for you to come out.
Funniest bit is that she will sometimes stop doing all that and go back to her maid duties ignoring you entirely.
She is a very interesting character whom I could write liken 200 paragraphs about but I genuinely think that everyone should play haunting ground (up until the end of her section and then drop it to watch a playthrough because it kinda falls off after that in the gameplay department)

Owlman from Justice League Crisis on Two Earths.
Normally Nihilism is just something that gets tacked onto villains as just another trait yo contrast the villain with the oh so hopeful hero. Rarely has there ever been a character written with the trait in mind, and a somewhat understandable philosophy. I do not wish to spoil as it is a good movie and it like the length of a single Columbo episode.
Anyway whenever someone says "It doesn't matter" the tinniest dinkiest Owlman pops into my head.

Joker from DC (from every piece of media that aren't the mainline comics after the release of The Killing joke) (I do not even count the Suicide Squad movie joker as a joker so he is disqualified immediately).
I have to make very specific classification whenever talking about Joker because how he's been written in the comics for the past 30+ years. Which is why I will have to put an asterisk next to any sentence where it doesn't apply to moder-ish mainline joker version ().
But the joker is one of those characters who are so good when they are being written correctly.
From the absolute menace and unpredictability of him when he's a side character in a major plot(). To the insane plans that he conducts when he Is the main villain of a story I think Joker brings a real sense of escalation to any story. Also gotta love his relationship with batman(). The way that he has a strange one sided affection in a way is really good and extra fascinating how some stories explore the whole dynamic()()()().
Harley Quinn is also one of my fave characters but frankly she doesn't quite classify as a villain these days and I actually think that her modern interpretations are well written unlike a certain clown prince of crime.

Kefka from Final Fantasy 6 is another evil clown but this time I do not have to put any asterisks.
Gotta love how fascinating Kefka's character is when it comes to how he interacts with the world around him. Like he's a war general he is respected, people clean his shoes till they shine in the middle of the desert because he said so. But also he is just a complete lunatic who literally poisons the water supply burns the crops and all other war crimes because he is just too respected for anyone to point those out. It would take too much effort to try and replace him so he is just allowed to exist. It is so well set up to the point where in retrospect when the [Big spoiler plot twist] happens it all makes sense. His speech durring [also spoilers] is very fascinating as in a way it shows what being only ever respected and feared yet not understood can do to a person.

Another one I also really like is-