The X-Men are a team of mutants that have always prided themselves on protecting a world that hates and fears them. The one thing that unites every member of these wayward teams: Mutations. Each and every long-term X-Man has possessed one mutation or another that sets them apart from the world at large.
But some mutants didn't just stop at one mutation. Years after their first mutations, some mutants experienced secondary mutations that granted them additional powers and skills. While some are minor or, in Husk's case, just changed her personality, other mutants gained real and powerful advantages from them.
Elixir
Elixir is one of the strongest mutants in Marvel comics. With a touch that can heal a human being so completely that it can regrow a heart, he managed to earn a place on the Krakoan team that has been resurrecting deceased mutants. Still, that isn't all that Elixir can do. He also possesses a touch that can harm anyone he touches — though he uses that much more sparingly.
Even with those amazing powers, he also has a secondary mutation that displays his state of mind to all those around him. After healing himself after a severe injury, he developed color-changing skin. When he heals other beings, his skin takes on a golden hue. When he harms them, it takes on jet-black ink-like color. It's a fairly harmless mutation, but when combined with his extraordinary abilities, it can make him an intimidating figure that can scare enemies into submission.
Beast
One of the first members of the X-Men, Beast originally didn't possess the blue fur that fans recognize so well today. Yet, after a few experiments, he developed an ape-like appearance that added some strength to his powerset. Still, a secondary mutation quickly granted him cat-like features, sharp claws, and sharp teeth that have added some extra ferocity to this Beast.
Given that Beast was always capable in a fight, having these new abilities gives him even more of an edge. After all, there's something to be said for having claws to help in a fight. Even if it makes him a little more vulnerable to catnip, it's a pretty helpful mutation.
Masque
A member of the Morlocks, one of Marvel's best mutant teams, Masque is a mutant who originally possessed the ability to manipulate the appearance of anyone he came across — with the exception of himself. Given his ghastly appearance, Masque quickly grew bitter and used his abilities only to harm those around him.
Eventually, though, Masque developed a secondary mutation that finally allowed him to shape his own skin. Now able to move his own organs and reshape his height, Masque has retained his appearance but still possesses powers that could rival even Mystique's. With the ability to shift others, Masque may just be the strongest Marvel shapeshifter.
Wolfsbane
What's better than a woman that can turn into a wolf? A woman that can turn into an entire wolf pack! While each wolf is not the same size as her ordinary transformation, Wolfsbane was able to develop a secondary mutation that granted her the ability to shapeshift into five small wolves.
While it won't help much against flying enemies or distance fighters, having an entire wolf pack under one person's command is too good to pass up. It makes her an extraordinary help in a fight and an especially great defender of her many friends and allies.
Nature Girl
Once considered a character best left to the background, Nature Girl has risen to prominence in the X-Men Green series. Exposure to Arakko has kickstarted a secondary mutation in the young woman, and it has caused some violent effects.
As her physical shape changes in line with her newfound powers, Nature Girl has discovered that she has the ability to draw strength from the animals around her. While it does kill the animal she is drawing from and she appears to need the animal's consent before borrowing strength, it is an extremely strong ability that helped her snap Wakandan handcuffs. It's likely her powers will only continue to grow, making it a fantastic secondary ability.
Archangel
Certainly not a man who was originally going to be included among the strongest X-Men, Warren Worthington III had two bright white, fluffy wings that let him take to the air. Unfortunately, that was about all he could do. He wasn't exactly doing much in fights. Though he was later granted a form that gave him offensive capabilities, it wasn't exactly a mutation, and he didn't enjoy using it.
That's why it was such a big deal when Archangel discovered that he had developed a secondary mutation that gave him healing blood. Now, rather than needing to contribute more violently in a fight, he could help ensure that his allies were safe. Though the method was somewhat disgusting, as he had to sprinkle his blood on them, it gave him the hope that he wouldn't need to keep his Archangel form to really contribute to the X-Men.
Black Tom
After being severely injured by Cable, Black Tom was healed after doctors used a wooden substance that was grafted into the villain's skin. It caused a secondary mutation that granted Black Tom the ability to manipulate plant life and to take on a plant-based form that helped him to resist most forces in a fight.
While he lost much of his secondary mutation from the M-Day disaster, Black Tom still has considerable ability to manipulate plants, which has made him an extremely helpful resource during the Krakoan era. Now using his powers for good, Black Tom has displayed impressive control and strength by relying on his relationship with the Earth.
Emma Frost
The mutant best known for her secondary mutation, Emma Frost originally manifested telepathy alone. While Emma wasn't the strongest telepathic mutant, she later developed an additional mutation after surviving the massacre at Genosha, now with the ability to turn her entire body into an organic diamond compound.
Though her diamond ability doesn't make her completely invulnerable, it certainly gives her a lot of power behind her punches. This mutation offered Emma an offensive capability she was sorely lacking, which makes her more viable in a fight. The only downside is that she can't use her telepathy in diamond form, so she still runs the risk of losing if she plays her cards wrong.
Iceman
Iceman wasn't always considered a powerful mutant. In his first outings as an X-Man and one of the first members of X-Factor, Iceman mostly just threw snowballs at the enemy. After having his body hijacked by Emma Frost, he grew considerably more powerful. Yet it was his secondary mutation that essentially made Iceman unkillable.
As long as Iceman is in his ice form, should he be torn to shreds, he can still bring himself back from the brink and return to life. Given that he doesn't need to be in his human form, this makes Iceman immortal long before the rest of mutantkind caught up to him. It's an incredibly powerful mutation and one that makes him enormously useful in a fight, even if it takes him time and considerable energy to regenerate.
Northstar and Aurora
Twin mutants separated shortly after their births by a series of tragic accidents, Northstar and Aurora were originally only aware that each possessed superspeed and flight powers. Shortly after meeting, however, they discovered that they could create a blinding light upon making skin-to-skin contact.
Yet, as the two went through a few unexpected experiments, they each gained a secondary mutation that allowed them to independently create concussive blasts of light. This mutation helped to make the twins less reliant on each other, while also increasing their offensive ability. Instead of one powerhouse team, the Beaubier twins are now two independent heroes who can take on armies practically single-handedly. And, when they work together, the twins can produce explosive light. That's one of the stronger package deals in comics.