Pandora

I go through statuses in the activity feed, then mark down the earliest status update I've seen the replies to. Then before clicking a status in the notifications, I know from the URL whether I've seen it before. And if it's a new one, I also mark that down.

Sounds time-consuming, but with 200 notifications, it's a lot faster than going through every notification one by one.

@Tacodidra it sounds like giving yourself a tough day XD

With that method, it probably takes two minutes to go through the notifications when it would otherwise take eight or something. But if the notifications pile up like they did a while ago (when I had more than 1000 after five days), I'll probably just give up on going through them.