Unity 4 had a cool feature where if you click on a mesh/texture/material in the Inspector, the thing will automatically be selected in the Project window. Unity 5 seems to be missing this feature or handles it differently.
Actually, one more thing to keep in mind is that objects with transparency will still detect your mouse clicks even if you’re fully transparent. You could have a fully invisible quad and still be able to click to select it in the scene. If you can’t select something by clicking it in the scene view, maybe you have a transparent object blocking it.