Alas, "Patch Tuesday" this week appeared to fix some things AND break some others. If you use Microsoft Outlook 2013 after you rebooted your machine and opened Outlook you may have noticed that your folders were missing.
Microsoft applied a patch identified as KB2817630 which fixed a whole bunch of things (see list here http://support.microsoft.com/kb/2817630) but inadvertently broke the folders in a couple of versions of Outlook 2013.
To get your folders back you will have to uninstall this update.
First go to Control Panel → Programs → Uninstall a program in Windows 8. I believe it is Programs and Features in Windows 7.
On the upper right there will be an option called View installed updates. Click it.
What you will have is a long list of updates that have been installed on your computer. Look down the list and in the section for Office 2013 you should see an entry with (KB2817630) in the description. You will probably see 2 entries.
Right-click on the first one and left-click on Uninstall.
When the dialog box appears left-click on Uninstall. It may take a while but it will uninstall. You may be asked to reboot when complete. Just for safety's sake go ahead and let it reboot.
When your computer starts again you will have to go through the process again (you do remember you saw 2 updates with that number). Find the remaining update KB2817630 and uninstall that as well. Again you may have to reboot.
Now when you reboot your folders should return.
There is a caveat. I understand they have removed the update from the set of updates they sent out, however I found that the next day my machine had dutifully re-installed what had been uninstalled the day before. Microsoft's technet article (http://blogs.technet.com/b/office_sustained_engineering/archive/2013/09/11/outlook-folder-pane-disappears-after-installing-september-2013-public-update.aspx) suggests that you may have to uninstall the update associated with KB2817347 as well.
If it continues to be a problem, well, you now know how to fix and you won't have to repeat it forever. MS is working on re-publishing the September Public Update so the problem shouldn't last long.