TrueCrypt : Open-Source Disk Encryption Software for Windows and Linux
TrueCrypt is an excellent open source disk encryption system. Users can encrypt entire filesystems, which are then on-the-fly encrypted/decrypted as needed without user intervention beyond entering their passphrase intially. A clever hidden volume feature allows you to hide a 2nd layer of particularly sensitive content with plausible deniability about whether it exists. Then if you are forced to give up your passphrase, you give them the first-level secret. Even with that, attackers cannot prove that a second level key even exists.
OpenVPN : A full-featured SSL VPN solution
OpenVPN is an open-source SSL VPN package which can accommodate a wide range of configurations, including remote access, site-to-site VPNs, WiFi security, and enterprise-scale remote access solutions with load balancing, failover, and fine-grained access-controls. OpenVPN implements OSI layer 2 or 3 secure network extension using the industry standard SSL/TLS protocol, supports flexible client authentication methods based on certificates, smart cards, and/or 2-factor authentication, and allows user or group-specific access control policies using firewall rules applied to the VPN virtual interface. OpenVPN uses OpenSSL as its primary cryptographic library.
Stunnel : A general-purpose SSL cryptographic wrapper
The stunnel program is designed to work as an SSL encryption wrapper between remote client and local (inetd-startable) or remote server. It can be used to add SSL functionality to commonly used inetd daemons like POP2, POP3, and IMAP servers without any changes in the programs’ code. It will negotiate an SSL connection using the OpenSSL or SSLeay libraries.
Tor : An anonymous Internet communication system
Tor is a toolset for a wide range of organizations and people that want to improve their safety and security on the Internet. Using Tor can help you anonymize web browsing and publishing, instant messaging, irc, ssh, and other applications that use the TCP protocol. Tor also provides a platform on which software developers can build new applications with built-in anonymity, safety, and privacy features. For a free cross-platform GUI, users recommend Vidalia
OpenSSL : The premier SSL/TLS encryption library
The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and open source toolkit implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library. The project is managed by a worldwide community of volunteers that use the Internet to communicate, plan, and develop the OpenSSL toolkit and its related documentation.
GnuPG / PGP : Secure your files and communication w/advanced encryption
PGP is the famous encryption program by Phil Zimmerman which helps secure your data from eavesdroppers and other risks. GnuPG is a very well-regarded open source implementation of the PGP standard (the actual executable is named gpg). While GnuPG is always free, PGP costs money for some uses.