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.