This is recommended when you suspect one or more of your hard disks to have bad sectors - that is, corrupted data. Running this program at boot will allow it to search for and find where there may be a problem and attempt to fix it. It's also a good idea to run this periodically just in case.
On a modern PC, you shouldn't need to run scandisk from a floppy; this is handled automatically on startup if the computer was not shut down correctly. If you're running an older system (such as Windows 95 or MS-DOS), you can run it about once a month but don't always need to use a floppy disk.
Usually you want to run scandisk whenever your system has had an error or a sudden shutdown. The type of shut down I'm referring to is a power outage or turning off your computer by just pressing the power button. Scandisk will try to correct the errors for you.
Always make sure to run the boot disk in safe mode. Serious damage could be done if you don't. The other thing is only run the boot disk if you are having serious computer issues that a regular defragment or virus scan will not solve. The boot disk is not for everyday issues.