Where are my content types?

If one day, for no apparent reason, you notice that your default SharePoint content types have disappeared, you may have made the simple, unwitting mistake of reusing a GUID in a custom content type.  This can cause a very confused SP server to hide all of your out-of-the-box content types. 

To see if this is the case, all you have to do is back your changes out gradually, i.e. remove your custom content types one at a time.  It's usually the last one you added, and as soon as you remove the offending content type, your OOTB content types will become visible again.