Another interesting thing about Batman villains is that most of them don't really have any actual superpowers. While Metropolis and Coast City are often overrun by wildly overpowered bad guys, Gotham is ruled by criminals who dress weird. One of the most notable examples is Two-Face (aka Harvey Dent), who must have the most miserable tailor in the world. A former close friend to Bruce Wayne, Two-Face went nuts after losing half of his face to an acid attack. His psyche fractured, he depended on a coin flip to make all of his decisions for him - the ultimate way to dictate the "fairness" of the universe. What truly makes him a formidable foe, though, is that his very existence represents Batman's failure. He was everything good about Gotham, and Batman was unable to protect him, and still unable to ever fully pull him back from the darkness that overtook his mind. Regardless of however crazy you are, though, who would ever think its okay to ruin two suits for each outfit?
The Green Goblin killed Spider-Man's first love, Gwen Stacy. That alone - one of the most unexpected and lasting deaths in comic book history - is probably enough to justify his spot on this list. Making matters worse, it was later revealed he had impregnated Gwen, leading to the birth of twins, prior to his killing her. And - most villainously of all - he had an integral role in the horrible, terrible, no-good Clone Saga of the early '90s, one of the worst stories in comic book history. If you haven't read it, it's even more frightening than Willem Dafoe in a Power Rangers costume.
The only entry on this list to not originate from the DC or Marvel comic universes, Shredder is unique - more than you probably know. The comic book version of Shredder (real name: Oroku Saki) had a much grittier existence than his cartoon counterpart - he nearly commit seppuku, he was decapitated, and he was a much more revenge-focused villain. Eventually he did come back as a shark, so it got a little less gritty from there on, but he was still one of the greatest foes any anthropomorphic turtles have ever encountered.
As his name indicates, Apocalypse is bad news. An ancient Egyptian and the first mutant ever, he's perhaps best known as the infinitely-powerful ruler of a dystopian future, where a techno-organic virus has ravaged civilization. Beyond being a superpowered immortal god-mutant, he's also responsible for the creation of many X-Men villains, such as the equally-subtly-named Mr. Sinister and Archangel (who eventually went back to being good, but who was briefly one of the Four Horsemen). And somehow he maintains a deeply held belief in "survival of the fittest", despite living in a world where no one ever stays dead for more than a few months.
Being the "God of Mischief" doesn't really seem all that threatening, but Loki is a master at lies, manipulation, and generally finding ways to get whatever he wants, despite his lack of brute strength and his insistence on wearing a really dumb helmet with giant horns. Not that Loki's trickery always works too well - he riled up the Hulk into causing havoc, which accidentally led to the creation of the Avengers. He transformed his foster brother Thor into a frog, which didn't last too long. And he was recently part of the Cabal - a secret supervillain organization. And what makes Loki so fun is that he is out not for good or evil, but simply himself, and is therefore not even trustworthy to his fellow villains, as he secretly tried to manipulate things to his advantage behind the scenes. He's come a long way from the guy who created the mask in The Mask.