Every graphical application installed in elementary will automatically put itself in the right category in the Applications menu. But what if you need to put a shortcut in there manually? It's easy!

1. Open the “Software Center” from the “Applications” menu or the dock.
2. Type alacarte, then install the single “Main Menu” app that shows up.
3. Hit Alt+F2 to open the “Run Application” window.
4. Type alacarte and hit Enter to open the menu editor.
5. Customize away!

Note: This guide is for the current stable version, elementary OS Jupiter.