Okay, so Superman has been around for decades. He's had hundreds of stories covering every stage of his life and the lives of the people around him. He's faced bizarre villains, countless alternate realities, and had more encounters with red kryptonite than you can imagine. He even had his own personal magical imp that would make regular appearances for the express purpose of causing mischief in the Man of Steel's life.
With all that, you'd think he'd have been turned into a woman more often, wouldn't you?
In fact, it doesn't seem to have happened very often at all. I've only been able to find a few stories which involved the Superman discovering his feminine side. (There have been some other TG transformations in the various Superman books, but they seem to avoid him almost completely.) In any case, I've compiled a few entries here involving the "last daughter of Krypton," with two of them being presented in their entirety.
(Note: There have been recurring rumors about a red-kryptonite story which causes Superman or Superboy to change gender. Several people seem to vaguely remember this story, but I've yet to find an actual account of the details, much less the story itself. If anybody out there has information, drop me a line and I'll be happy to share with the rest of the class.)
Claire Kent, Alias Super-Sister!
Superboy #78, Jan. 1960
This is probably the most well-known of the TG Superman stories, and it certainly has the most TG content. Superboy makes a crack about an alien woman's "driving" ability, and finds himself being taught a lesson about the fair sex.
The Turnabout Trap!
Superman #349, July 1980
Superman returns from outer space to find that everyone's gender has been reversed, but he's the only one who realizes it. Next to the "Super-Sister" story, this probably has the most TG content I've seen in a Superman story. It also features Superman using his "super-hypnosis," which narrowly edges out Super Sister's "super intution" as the goofiest power he's ever displayed.
Whom Gods Destroy
Superman/Wonder Woman: Whom Gods Destroy #4 of 4
In this Elseworlds story, the greek gods have taken an active hand in mankind's affairs, with Zeus and Hera playing complicated games against each other using humanity and their fellow gods as the playing pieces. Each of the gods has taken up opposing sides in this conflict, with the villains following Ares, who has constructed a fascist state with himself as the ruler. Among those opposing him are Superman and Wonder Woman (who in this reality is Lois Lane, having been granted her powers by the goddess Athena).
At one point during the conflict, Superman had been defeated and transformed into a centaur who debauched his way across the countryside accompanied by maenads (the female centaurs). At this point in the story, the heroes are staging the final raid against Ares' citadel, but to atone for his unwitting crimes against women, Superman must do so cast in the form of a teenage girl...