It has been more than fifteen years since the term Internet of Things (IoT) was introduced to the public. However, despite the efforts of research groups and innovative corporations, still today it is not possible to say that IoT is upon us. This is mainly due to the fact that a unified IoT architecture has not been yet clearly defined and there is no common agreement in defining protocols and standards for all IoT parts. The framework that current IoT platforms use consists mostly in technologies that partially fulfill some of the IoT requirements. While developers employ existing technologies to build the IoT, research groups are working on adapting protocols to the IoT in order to optimize communications. In this paper, we present and compare existing IoT application layer protocols as well as protocols that are utilized to connect the “things” but also end-user applications to the Internet. We highlight IETF’s CoAP, IBM’s MQTT, HTML 5’s Websocket among others, and we argue their suitability for the IoT by considering reliability, security, and energy consumption aspects. Finally, we provide our conclusions for the IoT application layer communications based on the study that we have conducted.