It's just a convention of referring specifically to a user within the stream of comments.
Twitter maxed it out popularity-wise, but it's been lingering mainly on blog comments where you would have the other commenters talking to each other and not being in a threaded view.
A recently completed feature request now means that the convention does something:
Normally, you only get notified of comments when you own the post.
You will now get notified of any comments that refer to you by @username in a comment, even if you do not own the post.
Only applies to other people in the comments that you are commenting on.
Response must include @username that you are referring to, where "username" is a reasonable match to the user's current display name (as seen in the comments above yours).
There must be a starts-with, case insensitive match of at least THREE characters to the displayname. So @a and @ab will never match anyone or anything.
Spaces cannot be used to match, so if the person's display name is "Peter Smith" then just use @peter to match.
Matching is performed in reverse chronological order, so if there are five people named "John" in the comments, writing "hey @john, have you considered apples?" will match the most recent John to comment.
Only one person can be replied to at a time in a comment. The first one "in" wins.