The past decade has witnessed the rapid evolution in blockchain technologies, which has attracted tremendous interests from both the research communities and industries. The blockchain network was originated from the Internet financial sector as a decentralized, immutable ledger system for transactional data ordering. Nowadays, it is envisioned as a powerful backbone/framework for decentralized data processing and data-driven self-organization in flat, open-access networks. In particular, the plausible characteristics of decentralization, immutability and self-organization are primarily owing to the unique decentralized consensus mechanisms introduced by blockchain networks. This survey is motivated by the lack of a comprehensive literature review on the development of decentralized consensus mechanisms in blockchain networks. In this survey, we provide a systematic vision of the organization of blockchain networks. By emphasizing the unique characteristics of incentivized consensus in blockchain networks, our in-depth review of the state-of-the-art consensus protocols is focused on both the perspective of distributed consensus system design and the perspective of incentive mechanism design. From a game-theoretic point of view, we also provide a thorough review on the strategy adoption for self-organization by the individual nodes in the blockchain backbone networks. Consequently, we provide a comprehensive survey on the emerging applications of the blockchain networks in a wide range of areas. We highlight our special interest in how the consensus mechanisms impact these applications. Finally, we discuss several open issues in the protocol design for blockchain consensus and the related potential research directions.