Magical Sailor Fuku

Since I didn't see one, as my first order of business I want to compile a list of games with any tg elements, however brief they may or may not be, and we can include crossdressing as well since tg is fairly rare in most games.

Perhaps the most famous - Final Fantasy 7's wallmarket sequence that I'm sure everyone knows about already
Divinity II Ego Draconis - You can alter the main character's appearance at any point after getting the tower, including sex
Mortal Kombat - Shang Tsung can transform into any character
[Prototype] - You can transform into anyone you absorb, including female civilians
Darkstalkers - Demitri's Midnight Bliss (as well as one of Anakaris' attacks) will turn the enemy into a girl temporarily
Cross Edge - Has Demitri and his Midnight Bliss as well
Fable II - There is a potion that changes the main characters' sex at the end of the game and sacrificing civilians at the temple of shadows can occasionally transform them into the opposite sex, which allows you to sacrifice them again if you so choose
Super Ghosts and Ghouls - Once you have the gold armor, if you get hit by the wizard in the box, you will be transformed into a girl temporarily
Jade Empire - At Lord Lao's furnace, the correct order of machines causes the main character to change sex temporarily (to one of the models of the opposite sex for a brief scene)
Disgaea, Makai Kingdom etc. - you can reincarnate a character into a different class


If you can think of anything I missed let me know. I'll also add more as I think of them.

Right off the top of my head, there's Faria. How it is applicable is kind of a spoiler, so... What do I do? :O

Startropics - A fortune teller transforms you into a girl so you can sneak into the females only Shecola

Zelda II - Fairy spell :P

ESP Galuda - The characters will change gender if the time-slow ability is used.

Ogre Battle 64 - This is borderline, but in this game soldiers in a battlegroup will be changed into female or male class, depending on the gender of the leader, once they gain enough experience. If the group possesses the Ansate Cross, soldiers will become the opposite gender.

Crystalis - NES - SNK

In this action RPG, at one point, the main character gets a polymorph spell, one form of which is a woman. These forms are unable to attack. The polymorph spell helps the hero by allowing him to go to the Amazon village.

Dead Rising - xbox 360 - capcom
This zombie survival game has some unflattering women's clothing Frank can change into. Provides no benefit mechanically, nor any change to story elements.

There are some amateur games that either feature or focus on TG themes, like Maelyn's games on pixiewink.net . Some Japanese VN's feature TG themes as well. Steins;Gate has the supporting character Ruka, who is a boy shrine maiden that wishes to be a girl.

In World of Warcraft, there is a place that the Val'krul, who are based off the Valkries of Norse Mythology, dwell, and the lead Valk'rul changes the player into a female Valk'rul to do a quest.

In the Undead (Forsaken) starting zone of Tirisfal Glades in Cataclysm Lady Sylvannus (the banshee Queen) enlists the aid of the Valk'rul to resserect the fallen humans at the graveyard. Also, you have to convince three recently undead npcs of their new (un)life, including a young lady who used to be a part of the Scarlet Crusade, now turned undead.