If you were to apply the laws of physics, several super hero's just really couldn't exist. Or really just exist at most levels.
Case in point, the Flash, or any other super speedster. Once you start accelerating, the only way for your atoms to hold together is to start absorbing energy around themselves. (Though most people think they just absorb gluons) But that creates a problem, since all atoms and structures have activation energies that make "windows." Basically putting they change their form, or create new forms. The Flash, if he were moving at say 30% the speed of light, would probably just be a floating mass of several super heated gasses, and would never reach the plasma stage, since he probably wouldn't last long enough. Same with Superman, or any other myriad of speedsters. And I won't use the infinite energy/mass theory here. But the same problem goes with energy wielders. Human Torch, when really powered up, would destroy his own mass, turning himself into gas, and there's a good chance Superman, being the nearly unlimited Solar battery he sometimes seems to be, would do the same just by standing in the sun. (Though chances are the energy build up eventually just cuts off at a natural point in all truth.) Now, superstrength could go around, since it kind of depends on the atomic bond structure to determine the actual durability of the mass at hand. Lifting tons of weight is something skin could never stand up to, obviously, but certain metals can.
As for low level energy beams, such as Cyclop's eye beams. Those sorts of energies exist. Red Sun energy is so much cooler than yellow sun energy. True, if it could melt steel, it SHOULD melt his head. Unless he had an errosive energy source close to, or part of, him that decreases heavy amounts of heat energy. Of course, his eye beams may simply charge atoms that it comes into contact with and fills them quickly to activation energies. But then, of course, he really shouldn't be able to hold that power since it would do the same thing to him. As for the recoil? Laser has near zero recoil. The "pressure" you feel from high end light sort of things, are really more like chemical composition change. Lightning would have little force, if it didn't change the air into plasma on the way down. You basically turn on light, light comes out, goes in one direction massless with little to zero recoil (measuring something that small is near impossible, so it's just assumed that light gives nigh none recoil force, though it's still there), and light just dissapates. (Let me restate that. Light GIVES recoil is small small quantities to atoms that have greater energy than the initial photon. Or else the photon is unresponsibe, and bounces without transfer of energy, so no recoil. So only bigger atoms gain "recoil" and that's only because they absorb the photons and just ALMOST continue the course, but since they're stronger than the initial photon, they just stray back. Hence recoil.) Lasers give pressure only because of the heat that's generated. The photons in lasers don't hurt you, the heat generated from the influx of photons into your atoms does.
Invisible Woman. Has to be refractive light structures. But really, I doubt you can move massless objects with your mind. Fundamental forces of the universe are only subject to it's corresponding nature. Photons (representative massless particle governing electromagnetic activity) are only attracted (for the most part) to electromagnetic sources. Unless, of course, that it started with a propellent force strong enough to send it in one or more directions. It's also repelled by it's own force. That's why light can be refracted or contained in a single room. (Turn on flashlight in room, it doesn't go through the wall.) But really, since it can't be slowed down or sped up, that lends to the idea that it can't be moved physically. So it's kind of... hard to say that she literally refracts light around herself. That would be more like... bending fabrics around yourself so that the space you occupy is so small, relatively, that you just seem invisible. But then you get into the whole invisible shield things and such, which lends to telekinesis, and I won't even go there. THAT'S a whole other issue to be discussed about.
Someone said the Vision I believe. He flat out DOESN'T work. You'd literally have to become smaller than sub particles, and unaffected by the four fundamental forces of the universe to be able to pass through solid objects. Or at least have enough energy in your atoms to simply overpower them. So, no. Vision just doesn't work.
Vibranium. A mass that can just absorb and dispel energy. If it did that, it couldn't really hold to itself, since the vibrational properties it has would just destabilize, and if something hit it, it would most likely bust up it's bonds. So yeah, one clump, but weak as crap in thought. OR, if it's vibrational properties just strengthen it's bonds (which would be most likely really) it just would be a REALLY hard piece of metal.
Captain America couldn't exist. But this has been covered in threads probably a billion times over by now.
Someone mentioned falling, so that's cool.
Hulk, or any other characters like him. The only CONCIEVABLE way, is that they pull in "Free roam" particles, that never gained any form, and he somehow reconnected them to create his mass. Though it would require such a ridiculous amount of particles, that he'd probably demolish something to do it at all, or cause things to explode as atoms broke apart as he stole particles from them. Mass conservation, pure and simple. Hulk is fun, he just couldn't exist. Question said that Ultimate Hulk is more likely. And while Ultimate Hulk is hungry immediately, and Question insinuated this, so I'm just restating it, Ultimate Hulk still couldn't work.
Nightcrawler. This is where the whole quantum physics thing REALLY gets into play. If string theory is true, he may just become out of tune, temporarily pulling his space, and the space of another dimension, into phase, and switching places. This would circumvent mass and energy conservation, and explain how he teleports. So if he's "strumming" around the "strings" he could concievably move at speeds that seem like teleporting when he comes back into vibrational sequence. So it wouldn't be miniwormholes, since he's technically not bending the "fabric" of reality to fold and match upon itself. And even if he did open them, the "holes" would be so small and short that it probably COULD only suck him in. But bending reality would require an immense amount of energy. The "suction power" of a black hole is directly proportional to it's size. Case in point, the man made particle sized one, it only drew particles toward it, and not even into it since it didn't last long enough. And it really didn't disturb it's "field" all that much. So Kurt making black holes isn't THAT far fetched. It's just the energy requirement. But it's more likely strings.
Magic. That would be outside of science. Or at least MAGIC magic would be. Such as making signs that breach dimensions and such. Since that really just breaks the laws of reality. If the fabric were that fragile, a kid who mumbles and draws circles would have destroyed Earth by now.
Though it's more biological. Healing characters. To heal quickly, they'd have to have the raw materials inside their body, and super fast cells that move several hundreds times normal cells. Basically, if they got their arm lobbed off, they NEED 45 lbs of material from another part of their body to fix it. I guess that's physics too, since it's a conservation thing. And someone mentioned Wolverine's bones. Veins and arteries move in and out of his bones. So unless they removed his skeleton, covered it, and did a bad job putting it back in, he's pretty safe in the blood cell department.
Vangard made a Spider Man thing. And I agree, except that it's most likely he sticks like most insects, via weak chemical residue bond. But through gloves? Or clothes? Doesn't happen. And his weight would probably bring down a few walls. Though not TOO many, since he's usually hanging off walls outdoors. It's just LANDING on them that gets me. If he flings himself up against most walls, that's a lot of concentrated force and mass hitting the wall.
Flight is loopy. Altering gravitons would require an immense energy source. It'd just be easier to say they used some form of anti graviton force. And they could empower it to just basically cause the graviton's superior energy to just thrust them places.
And... for now, I'm done.