E-mail services are the method of sending and receiving electronic messages over communication networks. Web services on the other hand provide a channel of accessing interlinked hypermeida via the World Wide Web. As these two methods of network communications turn into the most popular services over the Internet, applied cryptography and secure authentication protocols become indispensable in securing confidential data over public networks. In this chapter, we first review a number of cryptographic ciphers widely used in secure communication protocols. We then discuss and compare the popular trust system Web of Trust, the certificate standard X.509, and the standard for public key systems Public Key Infrastructure (PKI). Two secure e-mail standards, OpenPGP and S/MIME, are examined and compared. The de facto standard cryptographic protocol for e-commerce, Secure Socket Layer (SSL) / Transport Layer Security (TLS), and XML Security Standards for secure web services are also discussed.