There is a quick and easy way to clean this up, however….in fact, there are two ways.
The first way is to simply add your Applications folder to the right side of your Dock. After you do this you can Control+Click on the folder, and a menu will appear with our Applications neatly organized for your use.
BUT…if you have a ton of Apps in your Applications folder, that might not be efficient enough.
That leads us to the second solution. Create a new folder, and add aliases of the applications you use most frequently (but that aren’t in the Dock already). Then add this folder of aliases to the Dock. Control+Click….BOOM…all those applications are one click away.