For instance I just installed the Intel Graphics Update tool for this post, but the tool didn't install an icon in Applications. Do not despair.
One of the cool things about elementary and Linux in general is that it is highly customizable with just a little know-how.
I'm going to go through the process for adding a shortcut to the Intel Graphics driver to the Applications menu, but the same general steps can be used for any program you want to add.
1. Navigate to your home folder, then right-click and tick "Show Hidden files"
2. Then click into .local, then share, then applications.
3. Within this folder right click, then select New, then Empty File
4. Name the file anything-you-want.desktop. In this case, I named it intel.desktop
5. Then Open that file in Scratch (Right-click, Open in Scratch).
6. Paste the following in the file:
NOTE: These are just a few entries that can go into a .desktop file. There are many others that I have seen, but the ones here are the most common and will get the job done.
Name= Just put here whatever you want to call the file. For this example, I'm putting Intel Driver Update Tool
Exec= In this line, you want to put the command you would run in the terminal to open the program. For this example, I'll put: intel-graphics-update-tool
Comment= This is the place for a general descriptor that will display when you hover your mouse over the icon. Doesn't really matter what you put (or you could omit it entirely). I'll just put Update utility for Intel Graphics Driver
Icon= Add the path to the image you wish to display for the icon. In this case, the installer saved one here /usr/share/intel-graphics-update-tool/images/logo.png but it could be a path to anywhere on the system.
Version= Input the version of the program (or omit it.)
Type= I have always seen Application here.
Categories= Add here the categories that the application will appear in in Category view in the Applications
In this case I'll just add it to System Tools by adding System; to that line. So for my example, the completed file should look like this:
7. Save the file.
8. Now if you click on Applications and start typing "Intel" or click on the System Tools Category, you'll see the Intel Graphics tool. Click on it, and it will run!