For Unity, XFCE, and many more desktop environments, the files that cause programs to show up in your menus and Unity menus are in two places:
the latter especially for WINE
Sometimes an application might not show up in your menus nicely because it doesn’t have a
.desktop file in either of these locations.
Try opening one of the
.desktop files for a program that works, and saving as a new file, editing for a program you’d like to work the same way.