Application layer protocols are the protocols which applications most directly interacts with.
Protocols on this layer rely on the protocols on layers below to ensure messages get to their destination. What they focus on is the structure of that message and the data that it contain.
Application layer protocols can be thought of as a set of rules to define how applications talk to each other. Different type of application will have different rules, which means there are a lot of protocol on this layer. For example. the rules of communication for an email server is different than the rules of communication for a web server.
From the most popular protocols we can cite SMTP, FTP or the HyperText Transfer Protocol (HTTP).