The superpower of flight is bestowed by an organic jetpack that grows from overly-developed abdominal muscles. It's spelled out that fueling the organic jetpack requires a methane-rich diet, and that the power of flight does not grant immunity from the thin air of higher altitudes—those with the organic jetpack are invariably driven insane by the oxygen deprivation.
A fight with an opponent with a laser eye (a cyborg Frans Rayner) ended very quickly once the beam was fired and missed, leaving Frans too weak to fight. Why? The good Doctor noted that the eye had no outside power source, and was never used earlier in the fight, meaning it burns up a lot of calories.
Magellan - The level of secondary superpowers varies. One of the staff members has to wear an exoskeleton because she has super-strength but not super-durability. One of the early superheros, The Streaker suffers Clothing Damage when using his super-speed and resolves the problem by not wearing clothing. On the other hand, most of those with super-powers do sport Required Secondary Powers. Or maybe those who don't have them eliminate themselves.
Since most characters we see are superheros, or superheroes in training, perhaps those without the required secondary powers just didn't get past the strict selection process.
There is also a kind of magic water that allows blades to cut superhuman skin and hair, without superheroes wouldn't be able to shave.
Subverted horribly when a little girl with a very peculiar type of invulnerability has her powers temporarily disabled, she dies from opportunistic infections, and the doctors are unable to treat her with antibiotics once her powers return.
The teacher Miss Kyle has the ability to change her density. As her density increases, her size decreases. It was stated somewhere that she normally has a small amount of density increase at all times, converting a beautiful but petite woman into someone a little more than average.
If your powers can't draw on extra mass from somewhere, getting smaller as you get denser is exactly what should happen. Her strength shouldn't be anywhere near what it's shown getting to, but she should certainly be able to become at least a walking brick.
The Gym coach, aka Rockside, is a brick literally made of stone. He can't find a sneaker that can stand up to his weight and hence has to walk barefoot.
Harold Nelson's powers include being able to weaken or strengthen other people's superpowers. When used offensively he can increase people's powers beyond their control and potentially beyond the capacity of their requisite secondary powers to contain; this can be painful, inconvenient, or deadly (the girl who dies from infection example was a case where he shut down her powers for half an hour).
Another Gaming Comic crosses over into tabletop tropes with this: Pyromaniac Nuclear Dan, whose catchphrase is "I cast Fireball centered on myself!", had his roleplaying character briefly lack full immunity to his fire. Not wise enough to just stop casting centered on himself, said character took a few hitpoints of damage from every blast, inciting Dan to rage.
Dinosaur Comics discusses this, when T-Rex designes a game much like Super Mario Bros., except that the player character can't shoot fireballs from his hands without burning them.
In The Order of the Stick, Roy dons a belt of gender changing and becomes a bald girl, because if a "magic item doesn't specifically say it grows hair, it probably doesn't."
In a later strip, the heroes (sort-of-accidentally) defeat a hydra by decapitating it until it grows so many heads that it can't supply all of them with blood, causing it to pass out.
The Dasing Swordsman class are immune to all damage involving glass, so they can perform dramatic Super Window Jumps without hurting themselves. Elan demonstrates this also means he can punch through a window without injuring his hand.
The world of Mindmistress largely lacks these, although engineered powers (Mindmistress shows a distinct fondness for empowering individuals) frequently have them added in explicitly as technological measures.
"Grrl Power" has Achilles, a hero who is completely "proper, aggravating invincibility"-he can not be suffocated, drowned, poisoned, burned, frozen or injured by any force known. He is about 50% stronger than an average human, since he doesn't have to worry about breaking bones or tearing muscles. He has blocked a sword thrust with his eye. However, he does not have any anchoring effect, so enough force will knock him away from the battle, and it will just take time for him to get back. His teammates have used him to test their own powers or as a bowling ball.
It is later confirmed that some of Maxima's invulnerability comes from a sort of force field projected around her during combat. This explains how when she stood in an explosion she received no Clothing Damage while a good chunk of Achilles' outfit was burned away. A later attack does get through her main shield enough to tear away some of her clothes, but she was still mostly unharmed.