Complex 3D scene understanding has gained increasing attention, with scene encoding strategies built on top of visual foundation models playing a crucial role in this success. However, the optimal scene encoding strategies for various scenarios remain unclear, particularly compared to their image-based counterparts. To address this issue, we present the first comprehensive study that probes various visual encoding models for 3D scene understanding, identifying the strengths and limitations of each model across different scenarios. Our evaluation spans seven vision foundation encoders, including image, video, and 3D foundation models. We evaluate these models in four tasks: Vision-Language Scene Reasoning, Visual Grounding, Segmentation, and Registration, each focusing on different aspects of scene understanding. Our evaluation yields key intriguing findings: Unsupervised image foundation models demonstrate superior overall performance, video models excel in object-level tasks, diffusion models benefit geometric tasks, language-pretrained models show unexpected limitations in language-related tasks, and the mixture-of-vision-expert (MoVE) strategy leads to consistent performance improvement. These insights challenge some conventional understandings, provide novel perspectives on leveraging visual foundation models, and highlight the need for more flexible encoder selection in future vision-language and scene understanding tasks.