Personally I wonder if that's intentional and just more realistic to not offer an option to only mark selective items as read. I've seen many people with inboxes with hundreds of items marked as unread/todo which they will never ever read; same for any websites with these topbar notification items. Right now it's basically a "Go through all of your notifications now and check them, or admit that you won't take a look later at old ones anyway."

Currently you can go through whatever notifications interest you, skip the rest, and then "Mark All Read".

Not correct. I have 268 unread notifications and I don't want to be forced to go through all the old ones NOW just because some of them are useless. I want to remove the useless ones now so that at some point I'll get to the old ones too.

I don't care what other sites do, here we get stuff done. And precisely because most people don't know how to use email, we need to exploit web notifications as a tool for people to find old stuff they forgot but still need to look at. (We do the same in MediaWiki with $wgShowUpdatedMarker, btw; it's nice to see the same concept reused ten years later in phabricator.)

I ended up using "open all in tabs" to mark those 50 notifications as read, which actually would often open 3 links per row i.e. 150 in total, but in recent versions apparently got smarter and didn't open the "gilles" and "multimedia" duplicate links. However, many unlucky people are using substandard browsers or don't enjoy TabMixPlus on Firefox http://tmp.garyr.net ; using a Firefox extension shouldn't be required to make sense out of such a visible feature of our issue tracker.