Script Summary: Puts markers next to questions that haven't been read
For Stack Overflow, Server Fault, Super User, and Meta Stack Overflow, this will put an icon next to questions whose numbers are higher (that is, more recent) than that of the last question you marked as read.
Just click the icon next to a question in order to mark all questions up to and including that one as read.
Can also mark individual questions as read. Toggle in GM User Script Commands menu.
In the future, I may see if I can figure out how to recognize questions that have been moved back up, but it's probably not a huge deal.
Updates:
version 7:
individual question marking now turned on by default
version 6:
individual question marking was broken when done as first action
version 5:
bug fix; mark all read wasn't working
version 4:
Will now mark individual questions as read. Turned off by default; toggle in GM menu
version 3:
Fixed bug where I was comparing question numbers as strings instead of integers
version 2:
Fixed site detection RegExp. I forgot to escape my backslashes.
