Favorites remember everything except for the geometry. For example, they won't remember a wall layout, slab shape, text note, etc. IME favorites should be used for everything excpet where such geometry needs to be remembered.
Having said that, favorites are very specific when it comes to attributes, so if you're using files with different attributes, it is somewhat 'safer' to use pre-made elements, modules, etc. Then the attributes will be added to the project, if that's indeed what you want to do.
Best scenario is to have a tight template and base all projects off that. Then favorites are the way to go IME, and (the non-geometric) pre-made elements are obsolete.
My 2 cents.
Cheers,
Link.