TrueCrypt
Open Source
TrueCrypt is an open source software to encrypt volumes of data. It even supports the creation of virtual encrypted volumes which is portable.
CipherShed
Open Source
CipherShed is a planned source-available disk encryption program for on-the-fly encryption.
GnuPG
Open Source
GNU Privacy Guard (GnuPG or GPG) is a free software replacement for Symantecs PGP cryptographic software suite.
EncFS
Open Source
EncFS is a Free (LGPL) FUSE-based cryptographic filesystem. It transparently encrypts files, using an arbitrary directory as storage for the encrypted files.
Compare FreeOTFE with alternatives
Compare CipherShed and FreeOTFE and decide which is most suitable for you.