Mitsuko Kaucher
Mitsuko Kaucher voted up Skip Gentry's answer
Did you know the notification system is about fixed ? Just click on your notifications and then scroll down to "More notifications." Keep doing that and you will eventually get most if not all of them out. . Work in progress. 

I just checked mine. It' was up to 690. I scrolled through my notifications and it went to 663 and then it stopped and wouldn't show any more notifications. I'll try again later and see if I can get more off. It's good to know its being worked on. Thanks Rooster :)