Cmd-W - Same as Cmd-Q without the benefit of freeing up resources
If you close the main window, the app goes into a sort of suspention where it no longer updates itself.
I still cannot think of any justification for this, as the end result is pretty much equivalent to quitting the app all together only without the benefit of freeing up system resources...
I was told the only work around is to hit Command-H to hide the app as opposed to being able to click the close box on the window. In Mountain Lion, however, Command-H has no effect while the app is in Menubar only mode. This leaves the only work around to keep twitterrific checking for tweets without the window visible as being inoperable…
In version 3, not only would the app keep updating if you closed the window, but it had a nice feature where you could have the app auto hide itsself when you clicked on any other apps window in the background. I still feel the current version is lacking some of the basic features that made v3 as good as it was...
Bobby T. about Twitterrific for Twitter