This trope is for characters of any gender that have an alternate form or identity that is much sexier than their normal mode. It's not necessarily because their "civilian" mode is ugly, but it is generally more mundane or otherwise less appealing than their "heroic" mode. Depending on the genre, the changes can be accomplished through either regular means such as acting and swapping wardrobes or though various magical or phlebotinum-driven methods. This usually involves a change in a character's physical appearance, but sometimes it's purely a change in personality traits and behavior, suggesting that the character in question is deliberately making themselves appear unattractive to hide their Secret Identity.
Naturally, it often results in Loves My Alter Ego.
Given that sexual attractiveness is subjective, the best examples are those when the sexier nature of the alternate form is shown from the perspective of another character reacting to them with subtle flirting and innuendo that otherwise wouldn't be present. That said, it's generally pretty clear when the creators of the story are trying to change someone from Hollywood Homely (or even downright ugly) into Ms. Fanservice or Hello, Nurse!.
This often overlaps with Split Personality, Shapeshifting, Older Alter Ego, and Superpowered Alter Ego.
Compare A Darker Me. Compare also to Shapeshifting Seducer where a shapeshifter capable of assuming many forms takes on several in an attempt to appeal to a specific person. She Cleans Up Nicely should be used for when a character changes from their usually dull or unattractive wardobe, hairstyle and such to be more attractive (particularly at a formal event) however this new appearance is not associated with an alter ego or alternate physical form. Also see Evil Is Sexy.
See also Bishounen Line for when a villain gets sexier once they hit a certain power level.
The former case, which is called Nagi (Negi's father's name) by certain people, also ended up fooling Evangeline as well as infatuating Ako Izumi.
VampiricCute Witch Evangeline A.K. Mcdowell is a similar case. She has the body of a 10 year old girl, but uses magic to become older and very much The Vamp.
Chisame, a fairly normal looking, geeky girl, who combines cosplay, The Glasses Gotta Go and computer graphics editing to make herself into famous web idol Chiu. Eventually she gets an artifact that allows her to do much the same process magically.
Meru Puri - Aram is under a curse that causes him to age up to a teenager when exposed to the dark, likewise changing him from a cute boy to Bishōnen. Of course, to the girls in the manga, this might be viewed as a Cursed with Awesome ability.
In YuYu Hakusho, Koenma (usually in the form of an infant with a pacifier) is able to take on an older, more Bishounen appearance. Admittedly, an older more bishounen appearance with a pacifier, but its the thought that counts.
In Tenchi Muyo!Really 20,000 Years Old Washu Hakubi normally looks like a young teenager, and she pulls a fast one on Tenchi by unexpectedly transforming into her adult form to seduce him which is, needless to say, much more well endowed. The "alter ego" is her true form, but she's spent most of life in the younger form because she long ago decided that adult society was just too screwed up for her to want any part of.
Arguably applies to Sasame and Tsunami as well, although in this case it's more just growing up.
Tenjou Tenge has Maya Natsume, who actually inverts this trope. Her real form is that of a voluptuous young woman, but she spends most of her time is spent in the form of a young girl, making most people think it is her regular form.
"Bob? If that weird little girl suddenly turns into the kind of stacked voluptuous chick you’d see working in a sketchy nightclub, what should I do?"
When shy Aimi Komori applies her magic eye shadow, she becomes the sexy, superpowered cat burglar Shadow Lady.
In Zettai Karen Children, there's a Hospital Hottie who also happens to be a powerful Esper with powers of illusion. It's eventually revealed that her perky-and-pretty appearance is ALSO an illusion, which she maintains whenever anyone's around - underneath it, she's got a face straight out of a Hammer Horror movie - think 'Frankenstein' more than 'Dracula'.
Moka from Rosario + Vampire, when she transforms from Outer Moka into Inner Moka. This is especially evident in the anime where a lot of the transformation sequence is just her, um, various assets almost doubling in size. Also, inner Moka's voice is much more sultry than Outer's. Possibly a bit subverted later on because Inner Moka is actually the real one and Outer is the alter ego created to tone down her evil aura.
Spider-Man villain Stunner was an overweight and lonely receptionist who gained super strength and great beauty through virtual reality technology.
Black Cat considered Spider-man himself to be this, as she tried very hard to get romantic with him, but was not remotely attracted to Peter Parker, and consequently the big moment where he unmasked himself to her as a sign of commitment ended with her asking him to put his mask back on. In the Ultimate Marvel version she actually threw up, though this was just the Squick factor of realizing how young he was.
DC Character Looker was a frumpy librarian until she got her powers, and then she could turn into a redheaded hottie. Eventually, though, after she became a vampire, the sexy became her Shapeshifter Mode Lock.
Captain Marvel - Not that Billy Batson is ugly, but Cap is better looking (not to mention Not Jailbait). This is explained in comics set in the future that show that Captain Marvel is what he looks like as an adult.
Stanley Ipkiss, from The Mask film. Note that he's not more physically attractive (unless you're into that sort of thing), but more confident and impulsive (and gets reality warper powers), and that's why he gets the love interest in the end.
Actually the Mask only highlights personality traits already present, and brings out the ones the wearer keeps inside. Stanley, by the end of the film, has become a more confident and assertive person, meaning he had no need for the Mask anymore to become attractive to his love interest.
This was a main plot point in both versions of The Nutty Professor. In both versions, the titular professor invents a way to change him from a nerdy looking fellow in the original film (and a rather overweight guy in the remake) into a smooth ladies man. The original even concluded with the titular professor coming clean to a large group of people while he lets the formula wear off. There are no cuts, and both the professor and his alter ego were played by Jerry Lewis, so the transformation is almost entirely just Lewis changing his physical mannerisms and putting on a pair of glasses.
Anne Bowman from Psycho Beach Party (Chicklet's Split Personality) looks the exact same during her scenes but her confidence and behaviour, using her body language, makes her much more of a sex object than Chicklet's shy and Tomboy-behaviour. In-Universe, that is.
In God Stalk, the first volume of P.C. Hodgell's Chronicles of the Kencyrath, Jame's tavern dancer persona, the B'tyrr, is this. It's partly the rather revealing and sensual Senetha costume she wears, described as revealing "much skin in unexpected places", but also the dance, which is magically seductive. Since this is so not Jame's persona otherwise, people who've seen her as the dancer generally don't recognize her regular persona in public.
Live Action TV
Family Matters - Steve Urkel had a machine that turned him into Stefan Urquel, a sexier version of himself who was a smooth ladies' man without a hint of nerdiness. Later Stefan became permanent courtesy of Urkel cloning himself and using the clone to make the permanent Stefan.
The Are You Afraid of the Dark? episode "The Tale of the Dark Dragon" had two students taking a special serum that made them temporarily into their "true" selves (more good looking, confident etc). Once they were able to accept their deep psychological issues, the transformation became permanent.
Candice from Heroes casts illusions of her appearance (similar to Shapeshifting, but her shape doesn't really shift it just looks like it). She usually appears as a Hot Chick but her real appearance is a lumpy, acne covered mess named Betty.
In the Star Trek: The Original Series episode "Mudd's Women", Mudd has pills that he claims makes a woman more attractive. It was eventually revealed that a placebo produced the same results, with the Aesop being that attitude and confidence is what makes a woman attractive. Of course, given that they clearly showed women physically changing as a result of the pill rather than just acting differently, it was something of a Broken Aesop.
Jekyll: Most people seem to consider Tom Jackman's alter-ego Mr.Hyde to be considerably sexier than Jackman, with even two lesbian characters agreeing that he's hot. Katherine Reimer (Jackman and Hyde's assistant) is seemingly the only person who considers Jackman better looking than Hyde.
In La Fea Mas Bella, one of the many incarnations of Yo Soy Betty La Fea (Ugly Betty in the US), it turns out that the protagonist's ugliness is completely fabricated. Her alter ego, Aurora, is a model for the very same magazine where she works.
In Final Fantasy XIII-2, it's implied that Chocolina is actually this to Dajh's Chocobo chick. This is later confirmed in Sazh's DLC story. As it turns out, she got caught in the distortion just like he did, and wanted to help the others just like they always helped her, so Etro gave her the form of an attractive woman and the ability to be everywhere at once.
Bluster Kong in the CG Donkey Kong Country cartoon accidentally created a Nutty Professor type potion in one episode. It turned him from a sniveling, cowardly, balding ape into a smooth talking ladies' gorilla called Leo Luster. Candy Kong forgets about her date with DK and falls for him instantly. His coolness is so potent that he can use it to hypnotize King K. Rool and his goons into giving back the Crystal Coconut willingly. And he does it all through a catchy musical number!
Present in the W.I.T.C.H. television series as well as the comic above. Cornelia even wonders at one point if she can date older boys in her Guardian form. In Season Two does just that with Taranee's older brother.
On Recess, when Gus loses his glasses, all kids outside his small circle of friends no longer recognise him and mistake him for a new kid. He takes on a new cool kid identity, Guy, and several girls crush on him throughout the episode.