PGP and RSA protocols are the two widely used protocols in a number of servers and email applications for security with public/private key pair.
What is the difference between them? What other popular protocols are available?
Using a car analogy:
RSA is a public-key cryptosystem. That is, it is an algorithm for encrypting, decrypting and signing data using a set of two keys (the public key and private key).
PGP and GnuPG both offer the use of RSA for general purpose encryption and signing of data. They also offer other options, like Elgamal and DSA.
SSH uses RSA for authentication, not encryption. The server has your public key, and you have the private key, and SSH uses this fact to make sure you are, well, you. SSH also supports other keypairs, for example, ECDSA.
Further reading on the Information Security Stack Exchange:
And you should probably read What is the difference between SSL vs SSH? Which is more secure? as well.