If you have a modified console (CFW or PS3HEN), you can use tools like the Ultimate Toolbox . These tools install as a .pkg file and add a "Power Options" menu to your XMB, allowing you to trigger a rebuild without the "beep-holding" hassle of Safe Mode. HOW TO REBUILD YOUR PS3 DATABASE EASILY
Saved games, trophies (un-synced trophies might require resyncing), downloaded games, videos, photos, and system settings. ps3 database rebuild pkg
The only time you might use a specific PKG for database management is if you are a homebrew developer using advanced tools (like WebMAN MOD) to "refresh" the XML, but for general system maintenance, the official Recovery Mode is the safest and most effective method. If you have a modified console (CFW or