Hi Paul. If you're referring to the icon you have double clicked in order to install a program, then yes. You can either drag it to the trash can OR you can right click it and select "eject". Obviously though, the program icon its self should not be thrown away. This is the icon which you most likely either dragged to the "Applications" folder or which was created in said folder by default.
I've heard that in general it is not recommended that one move actual program icons outside of the "Applications" folder due to the nature of how OS X "permissions" work, as it can make things a bit wonky and you'll likely have to "repair permissions" in order to fix them.
I personally have a setup where there are folders specific to the type of applications within my Applications folder, (see screen shots) and it helps keep me organized... though is not necessary. It's just an OCD thing with me. If you need to find something in the applications folder from the dock, and you have it set up to view as a folder in "grid" view, you only have to start typing the name of the thing you're looking for and it will automatically go to it.
Otherwise, do not throw program icons away unless you want to delete the actual program! Be warned however, that SOME applications have an actual uninstaller, and that it should be used above throwing the icon in the trash, as the former method will get rid of extraneous files in an orderly fashion.
I also recommend getting an app such as "App Cleaner". What this does is hunt down any files or folders associated with the program you wish to delete/uninstall just to make sure there's no junk left over. It finds them, and puts them in your trash can for you to delete.
Doug
