jEncrypt is a commandline file encryption archiver. Files are encrypted with the AES-CTR mode, which was recommended by the National Institute of Standards and Technology in 2001 (NIST SP 800-38A). AES-CTR mode only provides confidentiality. It requires a message authentication code such as CBC-MAC to ensure an encrypted message is not accidentally modified or maliciously tampered with, which jEncrypt currently does not provide.
CryptSharp provides a number of password crypt algorithms: BCrypt, MD5 (and Apache's htpasswd variant), PHPass (WordPress, phpBB, Drupal), SHA256, SHA512, and Traditional and Extended DES. It also includes Blowfish, SCrypt, and PBKDF2 for any HMAC (.NET's built-in PBKDF2 implementation supports only SHA-1). If you are looking to store passwords, odds are CryptSharp will have the algorithm you want.
The WiKID Strong Authentication System is a highly scalable, secure two-factor authentication system. It is simple to implement and maintain, allows users to be validated automatically, requires no hardware tokens, has a simple API for application support (via Ruby, PHP, Java, COM, Python, etc.), supports multiple domains, and supports replication for fault tolerance and scalability. It also supports mutual /host and transaction authentication, wireless tokens only domains, locked tokens (to your PC), anti-keystroke logger keypad PIN entry, etc.