When you know someone a bit better then it shows more respect by referring to them by their name rather than a handle.
Additionally, I see most people doing it when they are talking directly to someone rather than to the group. As if I said "Chris, I find your post intriguing, but I don't understand why it is such an issue." Although there may be other people named Chris here, they message was for you and it's not worth my time to open up a PM to type out a response.
That all sounded a bit more coherant in my head, but I think that should give you the idea.
Personally, some of my friends actually call me Ness, because I (used to, at least) resemble the game character. My name is in my profile if you really want to call me by that, though.