This is a really good thread and I think it should be a sticky.
My Favorite Free Applications and Boot Discs:
Hirens Boot CD (9.5 is the latest official one)
Dariks Boot/Nuke CD (Good Boot disc for formatting drives, includes advanced security options where the drives data can be over written up to 35 Times making it unrecoverable)
CCleaner
Includes registry cleaner, data destruction feature, program uninstaller, etc.
Eusing Free Registry Cleaner:
Free registry cleaner with lot's of features such as backups, advanced search, etc.
TrueCrypt:
Encrypt files, Hard Drives, Flash Drives, etc. with advanced encryption (You can also encrypt your system files requiring a password to boot the system)