There will be notifications for all aspects of the site. So someActually, many category seem to be set up somewhat differently. Comments, for example, has no overall toggle. Tags has an overall toggle which is actually three radio buttons, with Off not being one of the choices.
At the bottom there's a section for "How You Get Notifications", and for example within the Email "category" there is a list recapitulating of all of the "What Notifications You Receive" categories, with an on/off toggle for each. That confused me at first but as it turns out that's just the same list of controls, grouped by how instead of by what. So that's actually cool.
This approach implies to me that you envision that the setting for a given category controls notifications for that category across all of one's subscriptions.
As I mentioned before, I think that will be a problem for categories that already have their own control mechanism, such as Messages. Even for categories where notifications don't currently exist (web activities) I think I'm likely to want per-group control of whether I receive an email notification about it. Just because I'm more interested in the doings of some groups than others.
I am all for having a completely configurable notification system, butMaybe "Web/App and Email" for any categories that already exist, to grandfather the user's current selections, and "Web/App only" for any new ones, so as not to suddenly create unexpected emails when a new category is created.