In Fushigi Yuugi Genbu Kaiden, Rimudo has the ability to switch between male and female forms (he usually stays male), but his Celestial Guardian abilities are only available when he's in his female form.
In Kämpfer, Natsuru Senou was chosen to become a Kämpfer. Thanks to this, Natsuru gains great strength and fighting abilities. On the other hand, it's apparently a rule that Kämpfers can only be girls, so any boys that are chosen transform into girls when their powers activate.
The Sailor Starlights from the anime version of Sailor Moon also count; their whole transformation sequence involves shifting out of a male form into a female one. (In the manga they were girls the whole time, merely posing as boys while in their civilian identities) and their princess is surprised to see they've chosen male civilian forms when they do find her making this an inversion, as their male civilian forms are not their birth gender.
Subverted with Itsuki Myoudouin from HeartCatch Pretty Cure!. Circumstances force her to live as a Bifauxnen, and it's after becoming Cure Sunshine that she slowly figures out what's best for herself. Namely, being both powerful and beautiful. Considering that her designated nemesis is an Ambiguously Gay guy with penchant for fashion, this might be a stealth queer aesop.
In PHD: Phantasy Degree, there are a set of magical rings that reverse the gender of their user as well as powering them up. Mostly used by a couple of women who turn into gorgeous, long-haired guys before bringing the hurt.
An interesting variant in Birdy the Mighty, where the protagonist doesn't really turns into a female superheroic version of himself, but is instead forced to be fused with a female Human Alien superheroine after she accidentally destroyed his original body. As a result, the two actually are separate characters, but share the same body and can switch between their respective appearance according to the situation.
Mahou Shounen Majorian is about two boys given Magical Girl powers by aliens. Their sexualities become pretty confused in short order.
From Philippine comics, Zsazsa Zaturnnah is an an effeminate homosexual and the proprietor of a small town beauty salon. He has a huge spiky stone that physically transforms him into a superhuman woman whenever he ingests it and shouts the word "Zaturnnah!". His female form is similar in both powers an appearance to Wonder Woman.
Mantra from The Ultraverse. Originally a male warrior, he gained magical powers after his soul was transferred into the body of a woman.
In The Savage Dragon, the power to turn into Mighty Man, a Captain MarvelExpy, passed on to Ann Stevens, a nurse who becomes a tall, blond, male superhero when she taps her wrists together.
In Alan Moore's Promethea, one of the former Prometheas was a male comic book artist called Bill Woolcott.
The HERO Dial in Dial H For Hero will, very rarely, turn a man into a female hero or a woman into a male hero; in the case of "Shocking Suzi", formerly Joe, he lost the dial before he could turn back and remained a superpowered woman for the rest of his life.
Espgaluda series: The heroes are already powerful psychics, but gender-changing makes them into even more powerful psychics.
Milton from Fable III is male; however, if the hero is female, Milton will swap genders when he assumes the hero's form, as well as gaining the power of a Hero.
In a disturbing variation, Morpheus from Dead-Aim seemingly changes gender when he mutates into an incredibly powerful Tyrant, with an obviously feminine voice, face and figure. The virus that mutated him is even called the TG-Virus. He gains super strength, speed, agility and electricity powers, but that electricity is produced by two organs on his chest that look like breasts. There is absolutely no reason for him to gain organic Combat Stilettos though. Considering what previous TG-Virus test subjects turned out like, Morpheus got off lucky with his new good looks and powers until he sustains too much damage and his Healing Factorgoes out of control...
Exposure to Virus-X gave the T-Girls of the Remix Comic version of Jet Dream low-level super powers (enhanced agility, strength, and endurance.) Their exposure was accidental, but a voluntary procedure for recruiting new T-Girls is also described.
In Jill Trent, She-Sir Science Sleuth, when Femavium interacts with the spinal fluid of a man, the result is a transformed woman with super powers that seem to vary according to the recipient. Jill gains "girl-brain cells with the proportional density of 58 girls." Another character gains "the flexibility of 45 ballerinas."
Whateley Academy has this as a central premise — in the WhateleyVerse, mutants have about a 1 in 3 to 1 in 6 chance of being Exemplars, and thus having what's called a BIT — Body Image Template. Long story short, these mutants have an idealized shape they associate with themselves, which can be just about anything — including the "wrong" gender. The majority of the stories revolve around a clique of students who had their genders changed during their origin stories, and are part of Poe Cottage — a dorm designed to hide this fact (as well as other LGBI students) from the study body at large.
Any male human who uses a female RIDE in the Free RID Ers universe is technically an example of this. Especially Rochelle who gains several seduction based powers after being Genderjacked by Uncia