Ho Yay: Genji has some moments with his friend and brother-in-law To no Chuujo. At certain point they dance together in a spring festival and spend some time after praising each other for their dance techniques.
Marty Stu: Genji: He's handsome, polite, educated, writes poetry, plays flute, can dance, can ride a horse and fight with a sword!
Nightmare Fuel: The "spirits" sequences, all the religious chantings sequences mixed with Lady Aoi's torments and Lady Rokujo's nightmare.
Squick: Genji's first kiss with his stepmother happens when he was only 12. It's important to remember that he has an Oedipus Complex with her.
Values Dissonance: The whole lifestyle of the prince would be considered outrageous on actual days, but back then, it was expected as part of a noble's life. Genji, therefore, exaggerates even for that time standards and some of his enemies try to use this against him.
Wangst: Genji whines, gets depressed and cries A LOT.