ALTERNATE VERSIONS
Ever wonder what had happened if not Cain Marko but Charles Xavier touched the Gem of Cyttorak? Well, there is one alternate reality, depicted in [What if (2nd series) #13], where exactly that happened. While Cain remained human and escaped from the crumbling temple ruins, it was Charles who became the Juggernaut and had to dig himself out for years. By the time he got free, Magneto had already recruited most known mutants of the era and started terrorizing humanity, but Juggernaut Xavier quickly defeated him and took over his mutant empire. From there, it quickly turned into a mutant tyrant regime and some of the more idealistic mutants among Xavier’s ranks felt this was not right. These few were approached by Cain Marko, who, in the meantime, had allied up with Magneto, for one single goal – get rid of Xavier. Eventually they succeeded, ejecting Juggernaut Xavier into open space, which is when human Cain realized that he was now at the mercy of Magneto, to whom he had no further use.
In the Age of Apocalypse, Professor Xavier died very early on, thus ending the constant feud between him and his stepbrother. With nobody to project his anger on, Cain Marko became somewhat of a pacifist and helped Destiny set up a secret community of humans and mutants alike, called Avalon and located somewhere in the Savage Land, that was undisturbed by the genetic wars raging all over Earth. Eventually, when they were discovered and Apocalypse dispatched his troops to destroy them, Cain found himself in the dilemma of being forced to fight while not wanting to injure any human being. The strain was too much for him causing a brain aneurysm to burst. Cain died immediately.
In another reality, shown in [What if (2nd series) #94], the Juggernaut’s temper got the better of him. In his first encounter with the X-Men, he killed Xavier and most of the X-Men, thus unknowingly dooming all of humanity and himself. There being no X-Men to realize the threat in time, the Sentinels were built in such a large number that they could overwhelm all super-powered individuals in a single strike. Next, due to their faulty programming, they released a lethal radiation to eliminate the source of mutation — humanity itself. Within a rather short while, the Juggernaut, protected by the enchantment of Cyttorak, found himself alone, everyone else dead. Only the Sentinels were still there but, over long months, he had defeated all of them. Just when Cain had lost all hope of ever seeing another human face, he learned of a secret underground community protected by Magneto. 
So determined to find someone to talk to, the Juggernaut broke through the protective walls around the community, thus exposing them to the radiation as well. Realizing that he had doomed the few people living there to slowly die of radiation poisoning, Cain headed back and left them alone.
While Prosh sent him on a mental journey through time, Cain also wound up in the body of his counterpart from an alternate future timeline, not unlike the Days of Future Past, in the year 2014. Apparently, Cain never became the Juggernaut in that reality, but he was still a fighter, being part of a rebel fraction fighting the Sentinels that ruled humans and mutants with an ironclad hand. Cain was using the equipment of several known superbeings, them apparently incapacitated or terminated, like Citizen V’s floating V-wing, some heavy weaponry and Klaw’s sonic weapon. Experiencing the life of this heroic version of himself somewhat triggered Cain’s need to redeem himself.
Cain found true happiness in the alternate future timeline MC-2, where he married attorney Sachi Yama and had a son, Zane, with her. He reformed and even joined the X-Men, though during one of the team’s last missions he chose to stay behind in another dimension to cover for the others’ safe escape. 
After long years of fighting the demons living there, Cain found his power sucked away from him, one of his foes’ doings, who wanted to use it for himself. However, something unpredicted happened and the Juggernaut power was transferred to his son, Zane, who still a teenager and was now able to switch between his regular look and a muscular Juggernaut form. Calling himself J2, he joined the Avengers in a redesigned version of his father’s armor, wearing one of his old shirts around the waist as a reminder of him. Eventually, he and the Defenders were even able to rescue his father from the demonic dimension. Needless to say, Cain was rather proud of his offspring.
In the Ultimate Universe, the Juggernaut — a young man in his late teens or early twenties — apparently wasn't empowered by mystical means, but was a superstrong mutant. Cain Marko, like many other young mutants, was forced to serve the Weapon X program for years, going on missions for them and fighting against his own kind, for example the X-Men, fostering in him a hatred towards humans and the belief that Magneto's Zero Tolerance policy towards humans was the right way. When the Brotherhood of Mutants attacked Weapon X and the former prisoners were released, Juggernaut was among those who joined the Brotherhood. Once the group was once again spearheaded by Magneto, Juggernaut and several other members committed terrorist acts. His cell of Brotherhood members was caught and incarcerated by the Ultimates. In the wake of the conflict with Magneto, it is unclear whether Juggernaut was set free like Rogue (though that is rather unlikely), or remained in jail until the eventual destruction of the Ultimate Universe.
In the House of M, Juggernaut remained attached to his then-traveling companion of Earth-616, Nocturne. The altered reality seemed to have trouble finding a place for the alternate dimensional daughter of the Scarlet Witch, 
leaving Juggernaut and Nocturne as a borderline amnesiac duo who were essentially a "glitch" in Wanda's new reality. Agents of the House of Magnus registered TJ as an unidentified genetic relation to Magneto, prompting a bounty on her head. Juggernaut defended his friend from the hunters and fell in with British royalty as Captain Britain and Psylocke fought to defend their borders from the unannounced mercenaries.
In a version of the Days of Future Past timeline, the Director of the Weapon X Program had Charles Xavier and the majority of the X-Men killed in the opening days of a Sentinel war on mutantkind. Wolverine survived the attack and wanted to put together a tougher, more aggressive team of X-Men to fight Weapon X's activities. 
Despite their history, Juggernaut decided that no one should be allowed to kill his step-brother but him, and joined Wolverine's X-Men against the Director. Wolverine's team fought alongside one another for five years, until they were betrayed by Agent Zero. Old post-hypnotic commands were activated in Zero by Weapon X, turning him against his comrades until he killed himself. Juggernaut and Wolverine survived the betrayal and reformed the X-Men yet again.
During X-Men: The End, the timeline jumped forward 20 years. Juggernaut was still loyal to Xavier's cause and operated out of the school as part of security for the mansion. When Stryfe, Genesis and the Goblin Queen attacked, Juggernaut rose to the defense along with Cargill, Kid Colossus, Polaris and more. He fought hard against Stryfe and beat down the villain before the Warskrull in Stryfe's form revealed its true form. A suicide bomber, the Warskrull set off a Shi'ar explosive on his chest, detonating the anti-matter reactor at the core of the mansion and levelling the entire area. Even the Juggernaut could not walk away from that, and Cain was later listed under the deceased.