Superman and Kryptonite
Surely everybody knows that Kryptonite is about the only thing that could strip Superman of his powers and, eventually, kill him. Lex Luthor, Metallo and even Batman have used this rare mineral in order to temporarily disable the Man of Steel.
The drawback is that any Kryptonian could become immune to kryptonite if he is exposed repeatedly. So, if the superhero isn't killed from the first time, then most definitely a second time wouldn't follow.
Red Light
Superman draws his power from Earth's young sun - because of the Sun's light, the Man of Steel can be considered invincible. However, when red light hits him, he becomes weak and has the power of, well, a normal human being.
Doctor Light is just one of the villains that could defeat the Man of Steel this way. In a way, Doctor Light (who can manipulate all ambient light) could drain all the powers from Superman, or could turn the yellow light from his body into red light, thus weakening and eventually killing him.
Telepathy
Of course, the Man of Steel has countless of powers, being basically a god among humans. But he still has a mind of his own, a mind which can be manipulated and overtaken by a powerful telepath (sure enough, he has taken several countermeasures over the time, training to resist powerful telepathic attacks, but still). And this telepath could be Manchester Black.
An even more powerful telepath could be Jesse Custer, who has this weird ability of commanding his own will on other people - at one time, he told a man to go f*** himself and that man went on and did that exactly.
Physical Strength
One word: Doomsday. This is the character that defeated and killed (sort of) Superman when they first met.
Magic
This is one of the other weaknesses of Superman: magic. When it comes to it, he isn’t invulnerable any longer. Sure enough, he is much more resilient than a normal human being, but still…
Read More: Marvel Characters Who Could Defeat Superman
Black Adam could definitely bring the Man of Steel down on his knees.
Lastly, just call Batman
There is a reason why Batman is one of the most beloved superheroes - he is capable of doing wondrous feats, even if he has no special ability and is just a simple human being.
As seen in Justice League: Doom (or the JLA: Tower of Babel storyline), Batman can defeat the entire Justice League on his own. He is a master strategist - so if one wants Superman killed, all one needs to do is call on Batman. The Dark Knight would figure out a way of bringing down Superman.
And Batman, for example, will use a green arrow – as in allying with Green Arrow, who will shoot a green-kryptonite arrow into Superman (as seen in The Dark Knight Returns).
