There really aren't any hard rules on this, but basically it boils down to: Is the object going to be moved or changed? If so, leave it off the base map so that it can be added by the GM.
Anything that gets in the way of the 'immersive' feeling that the VTT supplies should be left off such as grids and text.
Shadows/lighting is typically left off as those are dependent on what the PCs have with them. Also, with the newest version of MapTool, as an example, light sources can be assigned to objects so that the object radiates light. If you put in shadows and lighting they could conflict with what it should look like.
Definitely leave off NPCs or things that move about as those will likely be tokens that are added.