Doing so allow the user to know the program was not modified by other except the developer
Are you thinking about viruses? They usually wrap themselves around a program, so running the program will first run the virus. And then the original program, which will show the original certificate. People will think that MyDefrag is the virus....
A certificate is useful for commercial programs, which are protected by a serial number or something similar. The owner of the program does not want a hacker to remove that protection. A certificate will help there. This of course does not apply to MyDefrag.