I had this issue of “magento categories not showing”  from the first time i tried to get to know magento, and it happens in various circumstances.

The simplest one is when you do forget to mark a category as anchor.  In that case, it does not show up in the home page menu.

The other case is when you make your category outside of the default category tree. All your categories must be created under the default category parent tree node.

The third and more difficult case was when i deleted the default category for some reason. I recreated a root category and followed the instructions above, but with no luck.

The solution was to go to “System -> Manage Stores” and click on the Store Name. There is an option there where you can choose the right “default category” for the specific strore.