Top Alternatives to FreeOTFE

TrueCrypt is an open source software to encrypt volumes of data. It even supports the creation of virtual encrypted volumes which is portable.

GNU Privacy Guard (GnuPG or GPG) is a free software replacement for Symantecs PGP cryptographic software suite.

Steganos Privacy Suite includes file encryption, password management, and more.

DiskCryptor is a free and open-source full disk encryption system.

CipherShed is a planned source-available disk encryption program for on-the-fly encryption.

EncFS is a Free (LGPL) FUSE-based cryptographic filesystem. It transparently encrypts files, using an arbitrary directory as storage for the encrypted files.

LUKS is the standard for Linux hard disk encryption. By providing a standard on-disk-format, it does not only facilitate compatibility among distributions, but also provides secure management of multiple user passwords.

BitLocker is a full disk encryption feature included with Windows Vista and later. It is designed to protect data by providing encryption for entire volumes. By default, it uses the AES encryption algorithm in cipher block chaining (CBC) or XTS mode with a 128-bit or 256-bit key.

Seahorse is a GNOME application for managing encryption keys and passwords in the GnomeKeyring.