Batman Villains Who Would Destroy Spider-Man
Batman's no slouch. Even though he's a regular guy with a killer bod and a billion dollars worth of crime-fighting technology at his fingertips, he's still just a human schmo. Spider-Man, on the other hand, is a nerd who was given multiple superpowers via radioactive spider venom. These powers include, but are not limited to, the ability to predict danger, pick up cars, and to move with the agility of a thousand gazelles. Even though Spidey's earned his hero title, there are still plenty of Batman villains who could kick his spider-butt a few times before the ol' webhead would eventually find a way to clobber them back.
Man-Bat
Like Spider-Man, Man-Bat is a deformed product of science gone terribly wrong. Dr. Kirk Langstrom tried to harness the sonar powers of the average bat in a serum in an attempt to prevent his own hearing loss, but he failed miserably, transforming himself into a human-sized, enraged Chiropterae. Man-Bat has everything that Spidey has, in terms of strength and ability to hold his own in a fight, but only Man-Bat has fangs, a deep animalistic rage, and can fly. The only comparable Spider-Man foe is Vulture, and that guy is like a million years old.
Mr. Freeze
The tragic Victor Fries, as his name might suggest, commits only ice-themed crimes, and depends on a fancy robotic suit to survive in normal temperatures. Mr. Freeze has a pretty solid advantage over Spider-Man, since none of Spidey's usual villains really deal with the whole ice thing. Sure, there's lots of electricity, sand, and poison, but frozen water is generally out of the wall-crawler's purview. Try getting webs to stick to a frozen surface, Spidey. It's not gonna happen, and it'll probably take a while to sew up your anti-Freeze onesie.
Firefly
Continuing in the elemental theme, Spider-Man doesn't have too many bad guys who deal in fire, either. He fights guys who dress like rhinos, fishbowls, and quilts, but not many who deal exclusively in fire. Spider-Man himself has employed fire when fighting his many symbiote foes, but few have turned the tables. Spider-Man's costume is definitely not as fireproof as Batman's million-dollar duds, but Spidey's used his webbing to protect himself from fire in a few situations. Firefly would probably bring too much heat for Spidey to handle.
Clayface
There have been at least eight Batman villains named Clayface, and they've all had different powers, with one Clayface even manifesting symbiote powers similar to Spider-Man's arch-foe, Venom. Regardless of what form Clayface takes, he's always a better version of Sandman, Spidey's beach-based baddie. Shapeshifting and malleability might not phase Spidey anymore, but the ability to melt things with a touch and copy superpowers on top of the usual earthy mess would almost definitely catch Spider-Man off guard.
Bane
Simply put, if a villain can break a Bat, he can definitely break a Spider. Yes, Batman was weakened by a barrage of bad guys before Bane delivered the final crack, but Spider-Man would have to deal with all of that in addition to his dear Aunt May's meatloaf, whatever thankless job he has at the time, and paying his rent. It's probably a bit easier to face a villainous endurance challenge when you have a mansion waiting for you at the end of it all and not some sleazy Manhattan apartment. Bane would wear out Spider-Man and pop him in half like an action figure.
Killer Croc
Waylon Jones was born a monster. Every so often, a baby just pops out looking like it belongs in a pet store. While Spider-Man is familiar with fighting his own reptilian bad guy, Lizard, Killer Croc is a few levels above Spider-Man's usual grade of bad guy, since he has everything the ol' Lizard has, plus about 500 pounds of muscle. Lizard is a formidable foe, powerful enough to be one of Spidey's main rogues, but Killer Croc isn't called "Killer" for nothing. Croc could track Spidey through scent alone, and ultimately, reveal that Peter Parker is the man behind the mask.
Owlman
It goes without saying that Batman could kick the webbing out of Spider-Man, so an evil version of Batman from an alternate reality should be able to do the same, right? With the unexplained ability to cause confusion in others and an artificially-created super brain, Owlman would have all the advantages of your garden-variety Batman, but without the moral fortitude to let his enemies live. The result is one squashed spider.
Poison Ivy
Peter Parker's weakness for redheads is the single greatest tool in anyone's anti-spider arsenal. Batman might be an asexual crime-killing machine, but Spider-Man is seduced left and right by everyone from Black Cat to...every other lady in New York City, and Poison Ivy wouldn't even have to contend with the usual icy demeanor of Batman. Spidey would be a complete pushover for Poison Ivy's pheromone manipulation, and then her flesh-eating plants, and then as fertilizer. Green Goblin should have started wearing a wig years ago.
The Joker
The closest thing that Marvel Comics has to The Joker is Green Goblin, who is an incredibly formidable foe of Spider-Man due to his genius, mercilessness, and chemical manipulation of his own body. While The Joker and Green Goblin are both certifiable madman tacticians, the total unpredictable insanity of The Joker would definitely throw off the unaccustomed Spider-Man. At least Green Goblin usually has a complex purpose for his crimes, but the Joker's simple unpredictability and love of meaningless chaos would surely out-twist Spider-Man.