I had the exactly same problem after upgrading from 9.04 to 9.10. The
software center was installed but it was not showing up on any menus. I
didn't even know it existed until I did a clean install of 9.10 on a new
machine.

I found that I had an old version of 
/etc/xdg/menus/applications.menu
and upon upgrade the new version was installed as
/etc/xdg/menus/applications.menu.dpkg-dist

I saved off the old version, moved the new dpkg-dist version into place,
and the software center showed up immediately (along with more changes
to Applications/Games menus and probably some others).

I upgraded a long time ago, and probably responded 'keep the old
version' during the package install. I'm not sure what had been changed
in my original 9.04 applications.menu to prompt the question.

Hope this helps!
Mike

-- 
gnome-panel menu entry for software-center is missing
https://bugs.launchpad.net/bugs/477127
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