• Internet Cryptography
• SSH:   provides server and user authentication, confidentiality and integrity of messages. SSH is composed of several protocols. The SSH transport layer protocol typically runs on top of TCP/IP, it provides encryption, host authentication and integrity protection. SSH authentication protocol is a general user authentication protocol that runs on top of the SSH transport layer protocol. The SSH connection protocol, which runs on top of the SSH transport layer and authentication protocols, provides interactive login sessions, remote execution of commands, forwarded TCP/IP connections and forwarded X11 connections. Replaces telnet, ftp, rlogin, rsh, rcp, rdist.
  Free implementation: OpenSSH
• SSL v3.0:  two level protocol that is application protocol independent, allows confidentiality (with e.g. RC4), authentication (with e.g. RSA signature challenge) and reliability (with e.g. MACs constructed out of MD5, SHA1).
The lowest level, SSL Record, is built on top of a reliable transport protocol (e.g. TCP/IP), it is used for encapsulation of various higher level protocols (and does the encryption for example). One such encapsulated protocol is the SSL Handshake protocol, which allows the server and client to authenticate each other and to negociate an encryption algorithm and keys before the application protocol transmits or receives its first byte of data.
Free implementation: Open SSL
• TLS (rfc 2246): the successor of SSL v3.0.
• HTTPS: Standard that describes application of TLS to secure HTTP.
• IpSec: cryptographic security applied directly on IP packets, transparent to any application.
• Kerberos:  enables users and services to authenticate themselves to each other (also, a user needs to  enter his password only a single time per session to authenticate to multiple services).
• S/Key: one time password authentication scheme. In brief, server stores H_i(seed, password), only user knows password.  To authenticate to server, user provides i-1, H_{i-1}(seed, password), server verifies if H_i(seed, password) = H(H_{i-1}(seed, password)) and stores H_{i-1}(seed, password) for next time.  seed is there so that user can use the same password for different systems.
• S/MIME: provides authentication, message integrity, non-repudation of origin and privacy to MIME data.  Can be used by any mail user agent (MUA) supporting MIME or anything else transporting MIME data (such as HTTP).  Originally developed by RSA Data Security but standardization has now transitioned into IETF.  Popularized by RSA Security and it's used in Microsoft Outlook.
  
• PEM:  Privacy Enhanced Email, series of RFCs defining privacy enhancement mechanisms for electronic mail. Applies only to 7-bit text messages, became less important with the arrival of MIME which allows to add binary attachements to email. MOSS was an extension which didn't take off as S/MIME did.
• MOSS:  MIME Object Security Services. Provides services similar to S/MIME, but never became as popular.
• PGP:  Pretty Good Privacy, software that allows you to encrypt and sign files and emails, first written by Phil Zimmerman. You can get a freeware version at the International PGP home page, or a payed version at PGP Inc.  The most recent versions of PGP follow the OpenPGP standard described in RFC 2440.  GnuPG (GPG) is message formats have been standardized in RFC 2440.  The Gnu Privacy Guard (GPG) is free software (distributed under the GNU GPL) which is RFC 2440 compliant and acts as a replacement to PGP.  There is certain compatibility between GPG and recent versions of PGP.  For an interesting brief history of PGP see PGP Timeline.
  

• Cryptography APIs 
• Cryptoki:   also knwon as PKCS #11, is a crypto API that provides developpers abstraction from the device that implements the cryptography. Mechanisms are the various cryptographic algorithms, a token is a module that implements certain mechanisms and a slot is an abstract adaptor which holds a token. To access mechanisms one establishes a session with a token (a logical connection between an application and token).
  Free implementation: IBM's OpenCryptoki.
  Some commercial implementations (ex certain versions of Eracom ProtectHost Orange Hardware, Entrust Security Kernel, 3S Group Incorporated T2CSS) are FIPS 140 certified.
• GSS-API:    The Generic Security Service Application Program Interface (version 2 defined in RFC 2078).  A cryptographic API for distributed security services, allowing applications to authenticate each other and exchange messages security (data integrity and confidentiality).  GSS-API provides abstraction from the underlying mechanisms and technology allowing for source-level portability of applications to different environments.  Probably one of the oldest standard cryptographic API (dating back to 1993).  Popularized more recently by Kerberos version 5.0 (Kerberos v5 providing the underlying security mechanisms, see RFC 1964). There is an RFC for GSS-API C bindings and one for GSS-API Java bindings.  An extension of GSS-API is IDUP-GSS-AIP (Independant Data Unit Protection Generic Security Service API) for "applications requiring protection of generic data unit (such as file or message) in a way which is independent of the protection of any other data unit and independent of any concurrent contact with designated receivers of the data unit", RFC 2479.
  
• MS CAPI:  Microsoft`s crypto API. A CSP (cryptographic service provider) implements certain cryptographic functions, these can be accessed trough MS CAPI. MS CAPI includes functions that allow you to examine the CSPs that are on your machine. A CSP also stores key containers which are objects that hold the value of certain keys and the specifics of the algorithms they are used for. Several CSPs comme with Windows 2000. Microsoft has several CSPs that are FIPS 140 certified.
  Don't forget to see Peter Gutmann's attack on MS CAPI and some other Microsoft products
• CDSA: Common Data Security Architecture is a very big security middleware specification developped by Intel, with an open source reference implementation.  The Open Group adopted CDSA as an Open Group technical standard, you can get informatio about CDSA from them here.
  
• JCE. Java Cryptographic Extension, adds encryption, MAC and key exchange functionality to the Java Cryptographic Architecture (JCA), which defines an API for digital signatures, certificates and hash functions.
• Common Cryptographic Architecture. Cryptographic API implemented by several IBM products.

• Cryptography standards
  
• IEEE P1363:  Standard specifications for public-key cryptography.  Covers a wide range of things including cryptographic parameters and keys, key agreement, digital signatures and encryption based on discrete logarithm systems (like DH), elliptic curve discrete logarithm systems (like ECDH) and integer factorization systems (like RSA).
  
• PKCS:  Public Key Cryptography Standars published by RSA Security.  Includes standards for RSA encyrption and digital signatures, password-based cryptography, cryptographic message syntaxes (for messages that may have cryptography applied to it, for cryptographic keys and certificates, etc.), Cryptoki, etc.
• NIST FIPS and Special Publications 800 series:  Publications issued by the National Institute of Standards and Technology.  FIPS describe standards while SP 800 series describe recommendations.  Includes the Data Encryption Standard (DES) and Triple-DES, Advanced Encryption Standard (AES), Secure Hash Standard (SHA-1, etc.), Digital Signature Standard (DSA, etc.), standards and recommendation for symmetric key encryption modes of encryption, data authentication, entity authentication, key management, key escrow, security requirements for cryptographic modules (hardware and software), etc.
• ISO standards:  Includes several standards for cryptographic mecanisms.  Most are catalogued in ICS field 35.240.40 (IT applications in banking) as well as 35.040 (character sets and information coding).  The standards include mecanisms such as symmetric key encryption and message authentication, key management, entity authentication, etc.  Note, you have to pay to get a hold of these standards.
  
• ANSI X9:  ANSI standards for the financial services industry.  Includes standards for symmetric key encryption and message authentication, key management, digital signature algorithms, hash functions, etc.  You have to pay to get a hold of these standards.
  
• IETF RFCs:  There are several RFCs that standardize cryptographic mechanisms.  These include most of the protocols mentioned in the Internet Cryptography section above.
  

Note:  Many of these standards organization describe similar standards, and often base their standards on each other.
 For example, ANSI X9.30-1 and X9.30-2 describe DSA and SHA as per FIPS 186 and FIPS 180.  ISO 11568 series (key management) originated from X9.24.  A couple of these standards are listed in section 15.3 of the Handbook of applied cryptography.

• Key Agreement protocols (Note:   Key Agreement protocols are different from Key Exchange protocols, In a key exchange protocol, one side sends a precomputed-key to the other side, in a key agreement protocol, the two sides compute a new key. Many people confuse these terms, including OAKLEY`s RFC).
• KEA: NIST`s key agreement protocol, declassified since june 24th 1998, that uses Skipjack in it`s key derivation function.  It seems that the test vectors they gave are not good: see Lewis McCarthy`s page. You can get an HTML version of the spec here.
• IKE (rfc 2409): a hybrid between OAKLEY and SKEME, with the ISAKMP framework, used in IpSec. Sometimes referred to as ISAKMP/OAKLEY.
• ISAKMP (rfc 2408): General framework that defines procedures and packet formats to establish, negociate, modify and delete Security Associations (SA). Exact details are left to other protocols.
• OAKLEY (rfc 2412): slightly similar to STS, providing forward secrecy.  It utilizes cookies so as to provide a weak form of protection against denial of services attacks. Suggest some cool primes in the appendix (primes with lots of 1s at the beginning and end for some optimizations in computations plus a multiple of Pi in the middle to provide kosherazation.
• Photuris (rfc 2522): Uses cookies.
• SKEME (postscript): from Hugo Krawczyk.
• SKIP Simple Key Management for Internet, designed by Sun, based long term DH keys.