In Xfce's desktop menu, the programs that appear in the list under the divider under Settings are those that have a .desktop file in a couple of locations. I don't know what those locations are because I don't use the desktop menu much (I prefer to put program groups in the XFce panel, which I keep at the bottom of the screen). Other people can tell you what the locations are and how to create a .desktop file for an application you want to add to the system menu.
You can also add program launchers and icons to the desktop menu by clicking on Settings in the desktop menu, then on Menu Editor. You'll see three items above Settings in the editor: Terminal, File Manager, Web Browser. Right-click on one of those and click on Add Entry. Select Launcher for the type, then the name you want to see in the menu, then type or find the command that starts the program, then click on the button by Icons and select an icon for the program. If you don't want one of the icons offered, click on Image files by Select Icon From near the top. Then navigate to the directory where your desired icon is and double-click on it. Okay your way out and click on the Save icon near the top of the XFce4 Menu Editor.
That should do it. If there are programs in the system menu (Accessories, Development, Graphics, etc.) that you'd like to have accessible without going through the flyout, you can add them to the top or bottom of the menu the same way. It is very customizable.
This is a pretty abbreviated explanation. You can find out more by opening this location in a browser:
Hope that helps.