I agree that it would be nice to have fine-grained notifications synchronization across clients.
While looking to see if XMPP have such XEP, I found these extensions from Tigase that might be helpful in writing an official XEP:

https://xeps.tigase.net/docs/push-notifications/filters

I think this covers the specific use case of a push server, which unfortunately limits its scope.

For MUCs, it is a perfect fit for XEP-0402: PEP Native Bookmarks <extension>, in the spirit of XEP-0469: Bookmark Pinning? eg:

      <item id='theplay@conference.shakespeare.lit'>
        <conference xmlns='urn:xmpp:bookmarks:1'
                    name='The Play&apos;s the Thing'
                    autojoin='true'>
          <nick>JC</nick>
          <extensions>
            <notify xmlns='urn:xmpp:filter-notifications:0' when='always'/>
          </extensions>
        </conference>
      </item>

with when= taking 3 possible values "always", "never" and "on-mention".

For contacts, a PEP (XEP-0163: Personal Eventing Protocol) node would work. wouldn't it?

    <publish node='urn:xmpp:filter-notifications:0'>
      <item id='that-damn-guy@annoying.server'>
        <notify when='never'/>
      </item>
    </publish>

I am not entirely sure about the real life use-case for muting notifications from a contact when you can just block them via other ways, but maybe I'm just not imaginative enough. :)
List, any feedback on these ideas?

-- Nicolas