There was an element of Wraith: the Oblivion that I thought was absolutely brilliant. It occurred to a far lesser extent in Vampire: the Masquerade, and it's manifested a few times (but rarely) in games from companies other than What Wolf.
This element is the fact that supernatral powers of a specific type mark their user in specific ways. In Wraith, the masters of "Fatalism" seem to manifest arcane symbols on their foreheads, the Proctors (who master "Embody") end up with mattled patches on their skin from crossing the realms between the living and the dead, those who "Castigate" plunge their fingers into the souls of those around them to draw out the sin...and end up with permanently blackened/inky fingers from this, the harbngers end up with jet black eyes ... In Vampire, the healing/soul-manipulating/kickass-channeling-angelic-forces discipline of Obeah/Valeren, manifests as a scar on the forehead at the lowest levels, and as a character increases their mastery in this power this scar gradually evolves into a functional and mystical third eye.
I like this idea of marking characters permanently, I explored it a bit in the various iterations of Walkabout. In that game, characters would mark their bodies as a sign of sacrifice to certain spirits in exchange for heightened abilities in fields of influence related to those spirits. In this setting, some of the characters have already manifested specific "inhuman" appearances through the strength of their genetic heritage, but virtually all of the abilities that push a character to higher levels of power are derived from fungal symbiotes, mutations, or psychic attunement to otherworldly energies (and sometimes a combination of all three). Rarer types of empowerment might include a user fusing their soul to a rune weapon, implanting of ancient technologies, subversive transformations from within as Shellbrood toxins flow through a body... I can easily see each of these power types manifesting a specific type of physiological effect. The more the power is used, the stronger the physiological manifestation, some powers may be used to mask the appearances of others, but eventually everything is revealed.
This isn't a setting where the powerful people are all pretty. In fact the most powerful individuals in the setting tend to be the most inhuman appearing, not necessarily ugly, but certainly exotic. Some women might gain power through appearances, but there is certainly no desire for women to look "sexy" to attract men...in this setting it is the men who try to look pristine and capable of procreating, some subversive male groups may choose to engage the types of power that transform their appearance into inhuman forms in an attempt to take on the women as "equals", but general consensus among those who already have power follows a belief that using these benefits to elevate a man to a position of power is simply a waste of resources. There are certain bandit matriarchies where men are sent into battle and as raiding parties as a diversion from the true action happening elsewhere. In such groups it might be common practice to "milk a man of his seed" before sending him off to battle, those men who do something valorous might had their seed highly praised (and if they survive, they may be milked again in a few months when they recover enough to to back out again), those who die without honour might have their seed passed to the lower ranking females of society, and those who run away as cowards have their seed used as the focus of a magical ritual to hunt them down. The men look pretty and are the property of these groups, the women are the source of power.
I don't think these physiological transformations should be direct indicators of power ("Oh, she has a third eye, but it's not glowing when it opens, so she's definitely got mid level soul reaving"), instead I like the idea that these transformations become more prominent with regular use. Perhaps the female healing factor gradually causes these symptoms to subside if the powers deliberately aren't used. I also like the idea that different categories of powers might manifest their physiological effects in different ways. It might be too much to ask that every power does things differently, but on the other hand it seems too neat and tidy to make everything work exactly the same. Life is rarely neat and tidy, but people tend to like game mechanisms that are.
And for the moment I'll call these physiological changes "curses" (or maybe stigmata), and dividing them up by the three general types: fungal, mutant and psychic.
Generally, it will be a situation where every time a power is used, there is a chance that a related curse will manifest (or become worse). Different specific powers will have different specific curse manifestations.
Air - Surrounded by a cloud of spores, or smell of flowers
Earth - Bark-like skin, large size, or greyish extremities.
Fire - Smell of suphur, or high body temperature
Water - Constantly damp skin, or icy body temperature
Light - Faintly glowing skin, or intricate scar patterns
Dark - Black eyes, or blackened nails.
Air - White hair, or crackling with St. Elmo's fire.
Earth - Animalistic features, or metallic scales
Fire - Glowing red eyes, or tail
Water - Gills, or tentacle(s)
Light - Bleeding stigmata wounds, or
Dark - Shadowed patches on skin, or thin skeletal frame
Air - White eyes, slightly faded from reality, or clothes become tinted grey
Earth - Metallic teeth and nails, or clothes are eternally dirty and brown
Fire - Things near the character spontaneously combust, or clothes become tinted red
Water - Things near the character become damp if she stays too long, or clothes become tinted blue
Light - Halo, faint sound of singing follows the character, or clothes become faded and pale
Dark - No shadow, or clothes become darker/blackened
In each case, if a character fails an empowered action they may manifest a temporary curse to avoid any other backlash issues that might arise from the effect. If a character succeeds with an empowered action, they may give themselves over to the energies in the effect to gain an additional degree of success (thus obtaining a temporary curse). If a character has a curse already, they may increase it's duration, possibly even rendering it permanent. When a male accepts a curse, it is always permanent. Some powers may advanced levels...once you are afflicted by a curse, you instead get a new one that might have added benefits/penalties (much like the pure racial traits), and some have conflicting curses, they don't cancel each other out, but the most intense one takes precedence.
Just ideas at this stage, I'm sure they'll change in time. Any additional ideas for physiological power manifestations would be appreciated.