The best practices for handling and displaying 3D models and rendering in a desktop application include optimizing the 3D model file size, using efficient rendering techniques, implementing level of detail (LOD) systems, and providing user-friendly controls for interaction. It is crucial to ensure that the 3D model file is optimized by reducing unnecessary polygons, simplifying textures, and compressing the data. Efficient rendering techniques like culling, batching, and instancing can improve performance. Implementing LOD systems allows for rendering models at different levels of detail based on the distance from the camera. Providing user-friendly controls such as camera manipulation, object selection, and lighting adjustments enhances the overall user experience.