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Cryptographic Protocols
For protocols, try to use standard-conforming protocols such as SSL (soon to be TLS), SSH, IPSec, GnuPG/PGP, and Kerberos. Many of these overlap somewhat in functionality, but each has a ``specialty'' niche. SSL (soon to be TLS) is the primary method for protecting http (web) transactions. PGP-compatible protocols (implemented in PGP and GnuPG) are a primary method for securing email end-to-end. Kerberos is a primary method for securing and supporting authentication on a LAN, and for establishing shared secrets (thus, it needs to be used with other algorithms for the actual protection of communication). SSH is the primary method of securing ``remote terminals'' over an internet, e.g., telnet-like and X windows connections, though it's often used for securing other data streams too (such as CVS accesses). Note that there are two major versions of the SSH protocol, and there are several choices for key types and so on; see its documentation for more information. OpenSSH is an open source implementation of SSH. IPSec is the primary method for securing lower-level packets and ``all'' packets, so it's particularly useful for securing virtual private networks and remote machines. The new version of the Internet Protocol, IPv6, comes with IPSec ``built in,'' but IPSec also works with the more common IPv4 protocol.
Many of these protocols allow you to select a number of different algorithms, so you'll still need to pick reasonable defaults for algorithms (e.g., for encryption).
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