Themes like family and found family are quite common. Batman and Nightwing have a mentor - protege relationship which can be seen as a form of family. Harley Quinn, who is often an outsider, sometimes gets drawn into this dynamic. Power dynamics are also a theme. Batman has a lot of power and influence, and how Nightwing and Harley Quinn react to that, whether they challenge it or submit to it, is often explored in these fanfics.
One great 'batmanxnightwingxharly quin fanfic' is 'The Unlikely Alliance'. It shows an interesting dynamic between the three characters. Batman's brooding nature, Nightwing's acrobatic charm, and Harley Quinn's chaotic energy come together in a story full of action and unexpected alliances.