Save lists are not required for normal simulations. The Simulation Control dialog has a separate entry for save lists to be used during simulation. If you use a save list in a normal simulation, only those variables you specify will be saved. This can make model analysis quite difficult, therefore the use of save lists for normal simulations is intended only for very large models where the results are likely to require substantially more than 1 megabyte of disk storage. To use a save list in a regular simulation, add it in under the Advanced Tab of the Simulation Control dialog.
For variables that are not in the save list, only the terminal value for the variable will be stored. If you ask for a graph of such a variable it will be displayed as constant at the terminal value. If you are using custom graphs, it is very important to make sure that all the variables that will be graphed are included in the save list. For work in progress graphs this is especially true, because they will look quite funny if they are rescaled during a simulation and the values being graphed are not available.