A theme that pops up frequently is secrecy. Since their relationship is not something that would be easily accepted in the wizarding world, they often have to keep it a secret. This adds an element of tension and danger to the stories. Also, self - discovery is common. Both characters learn more about themselves and their true desires as they fall in love with someone they initially thought was their enemy.
The theme of forgiveness is also prevalent. Harry has to forgive Draco for all the wrongs he has done in the past, like his bullying and his family's association with Voldemort. And Draco has to forgive Harry for the times Gryffindors have looked down on Slytherins. Their relationship is built on mutual forgiveness and understanding, which is a key aspect in many of these fanfictions.
One common theme is redemption. Draco often has to overcome his past actions and beliefs as a Slytherin. For example, in many stories, he has to prove to Harry and others that he has changed. Another theme is the power of love to bridge differences. Harry, coming from Gryffindor values, and Draco from Slytherin, have to find common ground through their love for each other.