The easiest way to start is to think of what kind of apps you want and where they should be placed in your web pages. The type of apps is not that important, it's more important where they belong. You may have apps that are very general and not related to anything specific, like a messenger app. You may also have apps that are very specific, like a files app belonging to a specific page or section.
So the important thing will be to establish whether they belong to every page or maybe just to a specific section or if the app should only be visible to certain users. This will lead the way on how to group the apps. You should also remember that space can have many apps and that space can have several apps of the same kind if needed.