You will have to use a USB wire with your controller in Safe Mode (even if it is a wireless controller). Some non-Sony controllers will not work while in safe mode.
(If your PS3 can not beep due to broken speaker, the power light also flashs when the PS3 beeps.)
Restart System – This will exit Safe Mode and boot the PS3 normally.
Resore Default Settings – This will DELETE all PSN data! It will also reset all System Settings to default values.
Resore File System – This will attempt to fix file problems. It may take a while to complete.
Rebuild Database – This will attempt to fix database problems. It will DELETE messages, playlists, video playback resume info, and maybe other info. It may take a while to complete.
Resore PS3 System – This will FORMAT the PS3 hard drive! ALL DATA WILL BE DELETED!
System Update – Use this option to install System Updates (PS3UPDAT.PUP).