You express your concern for removing the programs as connected to the fact that they 'take up space' in the /Applications folder. Once deleted, re-intsalling applications that are OS components is rather challenging.
While you might think it is harmless to delete, say, Chess.app, and there is a good likelihood that you can delete it without adverse side effects, a future update to the operating system or a third-party program might rely on its presence for functionality. Some of these live in /System or /Library, but some required parts of the operating system live in /Applications. Mac OS X includes various components that it expects to find as part of the operating system.
