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I get notified for nothing! This notification center is crap.... Have to have applications to be open in order to be notified? So whats the point in it? Seriously biggest loss of this mountain lion!

The only app that has that limitation is Mail.
 
Not everyone gets the update notice at the same time. From Leopard on up sometimes I have gotten notified of updates at the same time I saw them posted online, other times it's been several days after.

In fact, I just got the NC update message for iMovie and Java a few minutes ago.
 
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