CrypTool 2

CrypTool 2 (CT2) is the successor of CrypTool 1, the most wide-spread free and open-source e-learning tool for cryptography and cryptanalysis. It has more than 200 cryptologic functions ranging from classic (like Caesar, Enigma) to modern (like AES, RSA, homomorphic encryption) crypto. It uses the concept of visual programming to present cryptographic processes; and it focuses on offering the according cryptanalysis methods too.
See this site for CrypTool 2, and this site for the whole CrypTool project.

Cryptii

Cryptii started as a little web app in 2009 by Fränz. Back then it was called FF Text Converter. In 2011 the project was finally renamed and moved to cryptii.com. Since it was featured on the Reddit frontpage in August 2015 – the 'Hug of Death' as they call it – it grew in popularity. It was completely redesigned and rewritten in 2017 introducing modular translation and encoding methods that can be chained together. Today the web app gets requested over 10k times a day while it is still under active development in the background.

quipqiup

quipqiup is a fast and automated cryptogram solver by Edwin Olson. It can solve simple substitution ciphers often found in newspapers, including puzzles like cryptoquips and patristocrats.

DECODE

DECODE involves the collection of ciphertexts and keys from Early Modern times, the systematic automatic detection of various cipher types, the development of algorithms for (semi-)automatic decryption of different types of ciphers, and the creation of language models and pattern dictionaries for early variants of fifteen European languages: Czech, Dutch, English, Finnish, French, German, Hungarian, Icelandic, Italian, Latin, Polish, Portuguese, Russian, Spanish, and Swedish.
See this site for the DECODE project.

Cryptobooks

Cryptobooks is an online bibliography of books about or dealing with cryptology from the 15th century until now. Its database contains more than 500 listed books and more than 350 listed authors.

Klaus Schmeh's Website

Klaus Schmeh's website offers a wide range of information about the history of cryptography, including unsolved crypto mysteries, ciphers & crime, a cryptologic travel guide, and picture galleries.
For more information visit the website .

Crypto Cellar

Crypto Cellar is a site dedicated to cryptology and cryptologic history with special focus on cipher machines and the cryptanalysis of these machines and other more complex cryptologic systems.
See this site for the Crypto Cellar project, and this site for the Crypto Cellar Tales blog.

Cryptiana

Cryptiana: Various codes and ciphers used through history are described.
See this site for more details.