It is said that a hero is only as good as their villain(s), and this goes double for those in capes. I was a True Believer growing up, but the Distinguished Competition always seemed to have an edge on the baddies, though Spidey and the X-Men did okay. There are some from both companies that matter to me, and even one from the Image of old. Here goes.
1. Mister Freeze - Batman
Granted, Victor Fries was a pointless thief with a thing for ice puns for long time, but Batman: The Animated Series gave him one of the greatest, most tragic backstories of any comics character. Said story (experimented with cryo-suspension to save his wife, only for it all to literally blow up in his face) was then retconned into the funny-books because it just flat worked. True, they flubbed it in Batman and Robin, but is there anything that movie didn't screw up?
2. Kingpin - Various Marvel books
He's just a cunning, intelligent gangster with no powers who often rules the Big Apple underworld, and sometimes even the city's "legitimate" side, despite opposition from major players of every moral standing. Punisher, Spider-Man, Daredevil and many others have gone up against the big fella, but his genius plans and fighting prowess have ensured he always comes back.
3. Clown/Violator - Spawn
Really the only memorable evildoer from Image's first go-round, this is basically the Joker given a Hellish make-over, a demon overseeing Spawn's work for Malebolgia whilst disguised as an utterly repulsive, well, clown. Except for when he's a gangly grey mess of horns and teeth. I like this one because of the design largely, but he was also much nastier than the demonic presences the Big Two ever presented. He felt like a legitimate denizen of Hell, and that's kind of a rare thing in comics.
4. The Lizard - Spider-Man
Another tragic character, Curt Connors experimented with lizard DNA to grow back a severed arm, only to become a giant sewer-dwelling alligator-ish beast. Yes, it's an amalgamation of Frankenstein and Doctor Jekyll and Mister Hyde, but a respected scientist dooming himself and his family through his own self-pity and misdirected genius is just a good story.
5. Mr. Mxyzpytlk - Superman
A Fifth-dimensional imp who can do anything and decides to make life heck for Our Boy in Blue just for funsies, I fell for this one because of Gilbert Gottfried on the Nineties cartoon, but the print version is just as sublimely ridiculous.
6. Juggernaut - X-Men
Not particularly complex, he's just the Prof's bully of a step-brother who became unstoppable when he found a mystical ruby. But I like that about him. Magneto's characterization on the page always felt scattershot, the world-threatening mutants like Apocalypse were often unintentionally silly, the whole Summers saga was a mess, and then you get a mean-spirited brute who, at first, just wants to steal things and be a dick. He was refreshing to me.
7. Doctor Doom - Fantastic Four
Maybe he'll eventually be done well in the movies, but I'm not holding my breath. I like him for the opposite reasons of Juggernaut; he is a fleshed-out megalomaniac. I mean, eventually. He started out as just another despot looking for world domination, but things have gotten a bit muddier over the years. Between the tragedies of his upbringing, his genuinely benevolent and competent rule of Latveria, and his firm belief that his ruling the world is all that will save humanity in the future (and he may be right...) makes him much more complex without ever quite being sympathetic.
There are a fair few missing, obviously, but most I never really cared for. Joker was another one that was inconsistently written (in the comics) to the point I couldn't really get invested in him, while Two-Face had a great origin and backstory but it couldn't compare to Freeze. Catwoman is often an anti-hero more than a villain and Harley Quinn is cool, but so much of her past treatment has been distasteful. Poison Ivy may have snuck onto the list, though; not only is she relateable and sultry, but her support and love for Harley has been one of my favorite things in comics for years. The fact that her villainy is mostly subpar cost her. Magneto's muddled, the various Goblins are silly as often as sinister, and the Vulture didn't work for me until Keaton brought him to life a couple years back. So yeah, you'll probably disagree with me. Feel free to tell me why.