Why has VirtualBox's menu disappeared?

Because you're in scale mode which causes it to be hidden.

Host + C is the toggle for scale mode (where Host is Right Control by default)

On Windows XP and Windows 7, as of Aug 2014, there's more to the story. To bring up the menu, and to be able to access all items on the menu:

1. If you're in scale mode, disable that with Host+c.
2. Bring up the menu by pressing Host+Home.
3. That will display the first of several menus. To get to additional menus, press the right arrow key.

I faced the same issue on my macbook pro and I found a solution:

A dirty workaround if using Ubuntu is to shut down all VirtualBox, and then edit the ~/.VirtualBox/VirtualBox.xml file. Find the line

<ExtraDataItem name="GUI/Toolbar" value="false"/>

and change the value to true.

If any process were still running when edited the file, the changes will most likely be gone once the processes update the file.

(Source)

In case you don't find this line (like in my case) simply add this line.

On OS X you can find VirtualBox.xml in /Users/<username>/Library/VirtualBox dir.