Pause menu
Groups can be useful with this kind of problem. If you group all code in groups, you can disable one set of groups and enable the other set when pause button is pressed.
The only problem with this is when you have to stop behaviors. Like objects which use platform, sine, physics behaviors. You can't access objects via behavior (at least I am not aware how). The solution would be to create one family per behavior, add family to each object using corresponding behavior and just disable these "behavior" families.
Unfortunately, families seem to be broken in current version. To be accurate, the game results with bug when I use more than one family per object.