USB Encryption: USB Safeguard is a free encryption tool for USB flash drives. It can be used to password protect any files that reside on your USB drive.
FreeOTFE is a Free On The Fly Encryption tool that can be used for Portable USB Encryption. The tool can be used to create encrypted volumes, virtual disks or entire partitions using AES, Blowfish, Serpent, Twofish encryption algorithms.
Remora USB Disk Guard is a free portable file encryption tool designed to encrypt files and folders on your USB flash drive or local hard disk. This portable application can be stored and run directly from any flash drive or portable storage device, requiring absolutely no installation.
USB Encryption: TrueCrypt is disk data encryption software that can be used to securely encrypt the information stored on hard disk partitions, portable storage media and USB flash devices. It can be run from a USB device in traveler mode.