Understanding scene contexts is crucial for machines to perform tasks and adapt prior knowledge in unseen or noisy 3D environments. As data-driven learning is intractable to comprehensively encapsulate diverse ranges of layouts and open spaces, we propose teaching machines to identify relational commonalities in 3D spaces. Instead of focusing on point-wise or object-wise representations, we introduce 3D scene analogies, which are smooth maps between 3D scene regions that align spatial relationships. Unlike well-studied single instance-level maps, these scene-level maps smoothly link large scene regions, potentially enabling unique applications in trajectory transfer in AR/VR, long demonstration transfer for imitation learning, and context-aware object rearrangement. To find 3D scene analogies, we propose neural contextual scene maps, which extract descriptor fields summarizing semantic and geometric contexts, and holistically align them in a coarse-to-fine manner for map estimation. This approach reduces reliance on individual feature points, making it robust to input noise or shape variations. Experiments demonstrate the effectiveness of our approach in identifying scene analogies and transferring trajectories or object placements in diverse indoor scenes, indicating its potential for robotics and AR/VR applications.