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".oo3" just means "this is an OmniOutliner 3 file". Most files on Mac OS X have a file name extension like that. ".mp3" is a sound recording, ".txt" is one kind of text file, and ".rtf" is another text file format.

Since this information is more useful to the computer than it is to most people, I believe Mac OS X defaults to hiding the extension. If you do a Get Info on a file, there's a checkbox in the "Name & Extension" section of the window that appears which controls that behavior. I suspect that OmniOutliner is also looking at that setting and showing/hiding the file name extension, as well.