Have a look at these questions over on Meta Stack Overflow:
How do comment @replies work?
Now that we have a global inbox, do we still need the Top Bar notifications?
From Stack Overflow Blog
The New Global Inbox
Well, I’m pleased to announce we’ve
added a new global inbox to every site
in our network. On the Stack Exchange
logo in the upper left hand corner,
the one you already know and love —
you may see a new, small red numeric
indicator light up:
That small red number tells you how
many new replies you have across the
entire Stack Exchange network of
websites. And by replies, I mean:
- New answers to your questions
- New comments on your posts
- @replies to you in comments
Click the number to go directly to the
global inbox.
At any given time, the inbox will
contain a list of the last 30 global
messages for your account, along with:
- The site icon, so you know which site the message is from
- The title of the question the message is associated with
- A preview excerpt of the first few characters of the message
- The relative age of the message (in a tooltip, so hover your mouse to see
it)