First of all, I'm not going to do some magic trick with Class-DB, if I need data before the database is available, then I'll use Settings.php (updateSettingsFile) to store it, rather than updateSettings...
Now, what should we store in the file...? enabled_plugins is a given... But I could also store a list of files that are to be modified by plugins. That's what I'm considering right now, but it might also be overkill... Remember, caching is to be done on all files when the cache is purged, but (1) once they're cached, files remain cached until you explicitly uncache or change plugin statuses, so it'll only slow down a few page loads and then the rest won't bother, (2) I don't know if it's worth loading a list of those modifiable files on every page load, when as I just said, it'll only be used once in a blue moon...
So, for now, I'll focus on just moving enabled_plugins to the settings file! ;)