There are many anime with crossdressing and Tg content but only few that have them as main theme.
They are
1. I My Me! Strawberry Eggs
Amawa Hibiki is a young man just out of college, with an education to be an athletics teacher. He's been having a hard time finding a job since he graduated, so all his money has gone towards living expenses. When his landlady demands his first payment to live in her living establishment upfront, he heads to the local middle school to get hired as a teacher. However, the principal refuses to hire him without hesitation. She will not hire men as teachers and makes it clear that she hates all men, saying they put no love into their passions and work. Amawa does not give up and with the help of his landlady, he crossdresses as a woman without a second thought, and gets hired, so he can earn money and also prove the principal wrong. Now, he has to keep his real gender a secret, and avoid strange situations, including the affections of his students (from both genders).
Link
http://www.anime44.com/category/strawberry-eggs
2. Otome wa Boku ni Koishiteru
Mizuho can't believe his ears when Grandpa's will is read out. Grandpa's
final wish is for Mizuho to attend the same academy as Mizuho's mother.
The catch is it's an all-girls school. With the help of friend Mariya
however, he gets a makeover good enough to fool everyone at the academy.
Link
3. Princess Princess
When beautiful Tooru transferred to an all-boys school, he received a
warm welcome...but little did he know that his new classmates had
nominated him for the academy's "Princess System." The lovely campus
"Princesses" must dress as girls (in frilly Gothic Lolita costumes) at
school events in order to lighten the stolid masculine atmosphere. Tooru
balks at first, but soon comes to realize the advantages of being a
"Princess."
Link
4. Maria Holic
The story centers on a sophomore named Kanako who enrolls in all-girls
school because she has a phobia of men and wants to find her destined
yuri partner. She meets a captivating freshman named Mariya who fits her
criteria — except her seemingly ideal mate happens to be a
cross-dressing sadistic boy.
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5. Hourou Musuko
Shuicihi Nitori appears to be a shy and quiet preteen boy, when
he transfers to a new school he quickly makes friends with the tomboyish
Yoshino Takatsuki who sits next to him. It soon becomes apparent that
both Shucihi and Yoshino are more than simply a sensitive boy and
masculine girl, they both are transgendered. Together they decide to
take the first steps toward becoming the people they want to be.
Link
6. Ranma 1/2
Ranma 1/2 revolves around a 16-year old boy named Ranma Saotome who was
trained from early childhood in martial arts. As a result of an accident
during a training journey, he is cursed to become a girl when splashed
with cold water, but hot water will change him back into a boy.
Link
7. Kampfer
Senou Natsuru is your normal, everyday high school student. However he´s
been chosen to be a Kampfer, who´s objective consists on fighting other
Kampfer with either guns, swords or magic, however, there´s catch;
first you can´t chose if you´re a Kampfer or not, and second, you must
have the body of a girl to use your powers.
Link
8. Kasimasi Girl Meets Girl
Hazumu was a shy boy who enjoyed gardening, collecting herbs, and long
walks in the mountains. One day he finally worked up the courage to
confess his love to Yasuna, but she rejected him. Feeling dejected, he
wandered up Mt. Kashimayama to the place where they first met to
reconsider his feelings. After getting lost, he wished upon a shooting
star which turned out to actually be a crashing alien spaceship.
Although he was hit by the falling ship, Hazumu survived the crash
thanks to some body reconstruction by the aliens, only they got it a
little wrong. Now that he is a she, Hazumu stumbles head-first back into
his social life and relationships only to find that the entire
landscape has changed.
Link
9. Cheeky Angel
Megumi-chan is a girl with a secret past. She used to be a boy until she
met a person she thought was a magic user. This person gave him/her a
magical book from which a genie appears to grant one wish when blood is
applied to it. Megumi made the wish to be a man in a man's body but the
genie has a twist: he grants wishes backwards so he turns Megumi-kun
aged 9 to Megumi-chan. Years pass and Megumi enters High School where
she immediately beats up the school bully who of course falls in love
with her. She is looking for that book again to be able to reverse the
spell placed upon her.
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