*.desktop text files that are used for menu entries. You need to create a new *.desktop file for your application and thats why I suggested you look into the existing files in /usr/share/applications for an idea on what you need to do. For example if your app is called foobar and its somewhere in your path such as /usr/local/bin, you can create something like
For the catergory part, look at entries for other apps in the same category and use that in your *.desktop file. If its a terminal program, make sure Terminal is set to true.