list the most powerful villains ever faced by the justice league
Superboy Prime is by far the most powerful lightyears.
Superboy-Prime possessed just about the same powers as his counterpart Superman although they appear to be more powerful due to his insanity. Superboy-Prime's power levels are reminiscent of the powerful Silver Age Superman, accomplishing such feats as overpowering two Supermen, punching planets with ease and defeating or killing many other DC heroes. Superboy-Prime also wears a yellow sun powered suit of armor to further enhance his power. His body is currently not energized with energy from a Guardian of The Universe, as he had used up his energy during his fight with Monarch.
He can fly at light-speed.
Prime can hear anything, anywhere like the Silver Age Superman.
Superboy-Prime can heal from wounds instantly.
He can generate an intense beam of heat to melt things and it was powerful enough to shoot through and penetrate the chest of Superman.
He can fly into a sun unharmed like the Silver Age Superman.Able to survive a guardian of the universe exploding. When he was charged by Oan energy, he was able to withstand monarch's attacks. He can eat uranium without any discomfort and withstood Krypto's heat vision, Powergirl and Supergirl's attack.
Prime has Silver Age Superman's powers to learn. He learned every Earth languages and 28 alien ones.
He can create hurricane, freeze foes or blow out stars.
He has Silver Age Superman's hypnotic skills.
He can move planets with ease and take on two Supermans at one time. He was able to hurt Sodam Yat who had the power of Ion and tear off Aquaman's arm.
He can travel faster than the speed of light or fly faster to cross the time barrier to travel back in time.
He can see through things except for lead.
Prime has Silver Age Superman's ventriloquism powers strong enough to speak to other contents.
Prime has x-ray, microscope vision and telescope vision that was strong enough to see across universes.
Prime like any Superman absorbs different forms of radiation and draws power from yellow sunlight, but appears to absorb it back faster and reach full power sooner. He has also been able to absorb the energy from a Guardian of The Universe and used it to increase his age, but only temporally.
Prime has a suit of armor that absorbs and stores Yellow Sunlight. As Prime has only been shown to wear the suit after he has been depowered, it is debatable as to whether it is used as a recovery suite or a power enhancer beyond his normal limit. However, it should be noted that Prime once indicated to his opponents that destroying the suite would not help because he was almost "whole again". This implies that he was in a weakened state at the time, most likely because he had spent several months trapped under a red sun. It has also been speculated that the suite provides a tactical advantage in case he has to fight at night or comes under attack from darkness-manipulating superheroes like Shadow Las.
The first incarnation of the armor, which was known only as "The Monitor Armor" was stolen from a museum that existed in a parallel universe which had somehow become trapped or replicated within The Speed Force.
But that first armor however was destroyed when the Supermen of New Earth and Earth-Two sent Prime flying into the Rao of New-Earth. The Sinestro Corps variant of the armor was designed by Prime, who was inspired to model it after The Anti-Monitor's Armor once he got a hold of the information that allowed him to see how his armor functioned. This version of the Armor was also destroyed during a battle with Earth's Heroes.
Shortly after his arrival in The 31st Century Prime got a hold of an exact and fully functional replica of his original armor that had been on a statue of him that was being sent into storage. The armor proved useful for a time but during Prime's fight with Superman and several L.O.S.H. members including two alternate versions of Cosmic Boy.
All of the armor save for the part covering his hips and the spandex uniform underneath were destroyed. Contrary to common belief, no version of this armor is capable of protecting Prime from the effects of Red Sunlight or powers that can reproduce the effects of Red Sunlight.
Time Trapper Powers
The immortal Time Trapper incarnation of Prime, who is much older than his modern day counterpart, has several abilities that his younger self does not. "Prime Trapper" has shown that he is not only capable of traveling through time without being seen but also manipulating it subtly as well. Prime also has displayed the ability to fire huge energy blasts and is somewhat well-versed in using psychic and psionic abilities. He can also cast an Astral Projection of himself into the minds of Future Seers such as The White Witch, is capable of manipulating his height at will and has the ability to control The Cockroaches that live with and on him at The End of Time.
Red Lantern Ring
Removing a red lantern ring causes death upon a user unless healed by a blue lantern ring. It is unknown if Prime truly wore a real red lantern ring during his temporary lantern empowerment while fighting various black lanterns. But if Prime truly wielded a real red lantern ring, his body was able to unwield the ring without suffering death.
Due to the fact Prime comes from another dimension the Kryptonite of New Earth has no effect on him. Also the reality-altering powers of 5th Dimension Imps does not seem to work on him. Originally, Prime was entirely resistant to Kryptonite because in his world Krypton was consumed by Rao, it's Sun, and thus Kryptonite never came to be in his reality making the weakness non-existent.
Recently however while in the "Threeboot" L.O.S.H.'s version of The 31st Century, he was actually poisoned with a large abundance of Kryptonite Radiation, the reason for this is unknown but it has been hinted that the "Threeboot" version of The 31st Century may actually be a reconstituted version of Earth-Prime.
Prior to this his only weakness was Red Sunlight like the other Supermen. Unlike the other Supermen however Prime is completely resistant to magic as shown when he said that it only tickled when Black Adam punched him multiple times with magic-enhanced strikes and also when the 31st Century version of Mordu the Mystical blasted him with a mystical attack.
Aside from those weaknesses Prime has many psychological phobias such as a fear of the dark due to the fact that it saps his cells of sunlight and an irrational fear of speedsters that has been deemed "Flash-Phobia", primarily because it was The Flash Family who imprisoned him in The Speed Force and then left him to rot under a Red Sun for approximately four years (Time in The Speed Force runs faster than on Earth.)
Prime is also afraid of being forgotten now that he has learned that in The 31st Century, everything he did during both Infinite Crisis and The Sinestro Corps War was incorrectly documented (i.e., Prime was supposedly defeated single-handedly by Kid Flash, Conner Kent and Sodam Yat during his fights with them) and that he has been considered only as having been minor annoyance to Superman whose place in History matters so little that his statue in the Hall of Villains at the Superman Museum was put in a closet and was about to be thrown into a real storage locker once the statue of the villain called Neutron had finished getting it's new paint job.