<strike>So I think what you're alluding to is that although Gnome Shell presents a version of the "Applications" menu, it doesn't (AFAIK) present the "System" menu anywhere.</strike>

So, you <strike>have to</strike> **still might want to**  add a launcher for the tool you want to run somewhere in the Applications menu tree.  That's easy but not trivial:

 1. click on your name up in the upper
    right hand corner
 2. click on "System Preferences..."
 3. click on "Main Menu" in the
    Look-and-Feel section of the
    "Control Center" that pops up
 4. select the section where you want to
    add the software-center launcher - I
    chose "system tools"
 5. click the "new item" button
 6. enter "software-center" as both the
    name and the command 
 7. click "ok"
 8. click "close"

Now when you select "Activities" in the upper left hand corner, then the "more" button just to the right of the word "Applications", you'll see your new software-center launcher listed in the system tools menu.  

I tried this and it worked perfectly.<br>-pbr

**EDIT:**  I don't know why I didn't see it there; it appears there's already a launcher for this; "Ubuntu Software Center" is a launcher in the "System" section of "System Preferences..." control center.  

**I haven't verified, but it looks to me like GnomeShell is presenting the Applications menu under that "more" button I mentioned above, and presenting the System menu within the control center that pops up when you choose "System Preferences..."**